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Sample GSM104741 Query DataSets for GSM104741
Status Public on Apr 30, 2006
Title CGH_replicate3
Sample type genomic
 
Channel 1
Source name genomic DNA, D.rerio
Organism Danio rerio
Characteristics Organism: Danio rerio
Tissue: caudal fin
Biomaterial provider Ashley R. Connolly
Extracted molecule genomic DNA
Extraction protocol CTAB DNA extraction
Label Cy5
Label protocol indirect dye coupling
 
Channel 2
Source name genomic DNA, P. moluccensis
Organism Pomacentrus moluccensis
Characteristics Organism: Pomacentrus moluccensis
Tissue: caudal fin
Sample ID: LD35
Biomaterial provider Karin S. Kassahn
Extracted molecule genomic DNA
Extraction protocol CTAB DNA extraction
Label Cy3
Label protocol indirect dye coupling
 
 
Hybridization protocol mixed labelled gDNA with 50ug human Cot-1, dried under reduced pressure.
hybridisation mix: 14ul formamide, 14ul 6.25*SSC, 0.6ul 10%SDS
hybridisation overnight in humidified chamber (1*SSC) at 42C
washing: 0.5*SSC/0.01% SDS, 0.5*SSC, 0.2*SSC
Scan protocol Axon GenePix 4000B scanner
Description comparative genomic DNA hybridisation experiment comparing hybridisation of D. rerio and P. moluccensis gDNA on a D. rerio oligonucleotide microarray
Data processing SPOT software
 
Submission date Apr 10, 2006
Last update date Apr 27, 2006
Contact name Karin Sonja Kassahn
E-mail(s) k.kassahn@imb.uq.edu.au
Phone +61 7 3346 2606
Fax +61 7 3346 2101
Organization name University of Queensland
Department Institute for Molecular Bioscience
Lab Ragan Group
Street address Queensland Bioscience Precinct
City Brisbane
State/province QLD
ZIP/Postal code 4072
Country Australia
 
Platform ID GPL3365
Series (1)
GSE4047 Danio rerio and Pomacentrus moluccensis: comparative genomic hybridisation and early gene response to heat stress

Data table header descriptions
ID_REF
prenorm_VALUE The prenormalized base-2 log of the background-adjusted ratio, R/G, using R/Gmedian for spot value and morphR/G for background.
VALUE The _normalized_ base-2 log of the background-adjusted ratio, R/G, using R/Gmedian for spot value and morphR/G for background; normalised across samples.VALUE normalised across samples
grid.r grid row
grid.c grid column
spot.r spot row
spot.c spot column
area The number of pixels in the segmented spot.
Gmean The average pixel value within the spot: green band.
Gmedian The median pixel value within the spot: green band.
GIQR The interquartile range of the logged pixel values within the spot: green band.
Rmean The average pixel value within the spot: red band.
Rmedian The median pixel value within the spot: red band.
RIQR The interquartile range of the logged pixel values within the spot: red band.
bgGmean The average pixel value in the background region: green band.
bgGmed The median pixel value in the background region: green band.
bgGSD The interquartile range of the logged pixel values in the background region: green band.
bgRmean The average pixel value in the background region: red band.
bgRmed The median pixel value in the background region: red band.
bgRSD The interquartile range of the logged pixel values in the background region: red band.
valleyG Median of median image values in four neighbouring "valley" regions: green band. "Valley" regions are square regions between spots.
valleyR Median of median image values in four neighbouring "valley" regions: red band.
morphG Value of a morphological opening of the green band image at the nominal spot centre. Openings and erosions (see below) use a rectangular structuring element with side lengths equal to twice the average horizontal and vertical distances between spots.
morphG.erode Value of a morphological erosion of the green band image at the nominal spot centre.
morphG.close.open Value of a morphological closing followed by a morphological opening of the green band image at the nominal spot centre.
morphR Value of a morphological opening of the red band image at the nominal spot centre.
morphR.erode Value of a morphological erosion of the red band image at the nominal spot centre.
morphR.close.open Value of a morphological closing followed by a morphological opening of the red band image at the nominal spot centre.
perimeter The perimeter of the spot as measured by the number of pixels in the spot which have a neighbouring pixel outside the spot. Each pixel is considered to have 8 neighbours in this process.
circularity A measure of circularity of the spot equal to area times four pi divided by perimeter squared. This is ideally one for circles and more than one for other shapes.
badspot A flag which is one if the spot area is greater than the product of the horizontal and vertical average spot separations, and zero otherwise.
nominal.center.row nominal center row
nominal.center.col nominal center column

Data table
ID_REF prenorm_VALUE VALUE grid.r grid.c spot.r spot.c area Gmean Gmedian GIQR Rmean Rmedian RIQR bgGmean bgGmed bgGSD bgRmean bgRmed bgRSD valleyG valleyR morphG morphG.erode morphG.close.open morphR morphR.erode morphR.close.open perimeter circularity badspot nominal.center.row nominal.center.col
1 -0.492018857 0.105912 1 1 1 1 127 1343.732283 1375 0.313288636 962.2204724 975 0.451985124 157.0314136 120 0.609996812 116.1727749 92 1.05444107 120 82 15 10 111 8 0 64 48 0.692677547 0 56 54.9047619
2 -0.185567111 0.202322 1 1 1 2 121 4659.363636 4957 0.285533052 4250.809917 4350 0.22500903 247.1348315 141 0.740400065 218 98 1.212556548 132 84 19 15 111 8 8 72 46 0.718587356 0 56 72.9047619
3 -0.279289322 0.196179 1 1 1 3 117 2414.598291 2536 0.352135037 2005.709402 2082 0.329920207 202.8967391 141 0.607018027 159.298913 92 1.134979933 128 96 19 19 122 8 0 72 46 0.694832402 0 56 90.9047619
4 -0.248008433 0.203043 1 1 1 4 135 3192.281481 3362 0.246860078 2745.792593 2816 0.294508038 191.2542373 136 0.624518674 160.5988701 88 1.060871961 115 88 19 19 122 1 0 80 48 0.736310778 0 56 108.9047619
5 -0.731637075 -0.056342 1 1 1 5 126 1086.642857 1100 0.2855476 670.6984127 658 0.523776027 180.8628571 137 0.678033543 114.32 90 1.098612289 127 84 19 0 122 7 0 80 46 0.748281048 0 56 126.9047619
6 -0.952212101 -0.147836 1 1 1 6 117 786.1880342 785 0.331473856 413.4273504 406 0.574719607 156.4619565 135 0.64462014 92.86956522 82 0.836248024 127 84 13 0 121 7 0 80 45 0.726056969 0 56 144.9047619
7 -0.381393035 0.089089 1 1 1 7 130 2083.461538 2118 0.284303691 1592.823077 1623 0.348841311 171.121547 124 0.659245629 135.7734807 78 1.297214731 108 71 13 9 119 7 0 74 46 0.772036002 0 56 162.9047619
8 -0.998172647 -0.163089 1 1 1 8 113 793.4070796 804 0.331279668 412.5221239 401 0.53121436 136.4361702 116 0.60077386 103.537234 86 0.988155293 99 85 15 10 114 6 0 77 47 0.642824753 0 56 180.9047619
9 -0.811097324 -0.216460 1 1 1 9 116 1181.956897 1173 0.28178235 680.3965517 666 0.413443058 155.7379679 126 0.591364486 98.53475936 88 1.07562277 109 84 15 10 105 6 0 77 47 0.659890897 0 56 198.9047619
10 -1.323539145 -0.604183 1 1 1 10 116 909.9224138 911 0.35464586 383.5689655 364 0.471323181 138.8888889 120 0.68117099 93.56111111 77 1.068534833 109 77 15 7 105 6 0 77 44 0.752943694 0 56 216.9047619
11 -0.362790937 -0.006176 1 1 1 11 121 3571.694215 3747 0.263319374 2800.280992 2910 0.295369749 164.172043 122 0.64607967 140.2956989 95 0.990398704 99 82 14 7 105 7 0 79 46 0.718587356 0 56 234.9047619
12 -0.699705976 -0.094835 1 1 1 12 115 1639.156522 1734 0.270745832 1085.678261 1066 0.507182632 151.6141304 118 0.753771802 110.9184783 83 0.923953605 94 82 14 14 107 7 0 79 45 0.713645739 0 56 252.9047619
13 -0.940739726 -0.122071 1 1 1 13 123 799.6585366 801 0.274609991 429.8780488 417 0.523496684 140.4519774 120 0.662933402 94.19774011 85 0.912200747 128 83 14 10 107 7 0 79 46 0.730464832 0 56 270.9047619
14 -0.140436499 0.267572 1 1 1 14 100 3233.84 3312 0.223606867 2898.68 2997 0.284078465 174.5119048 116 0.687449159 144.7380952 86 0.983230215 128 91 13 10 107 4 0 78 40 0.785398163 0 56 288.9047619
15 -0.889068009 -0.358853 1 1 1 15 106 1148.622642 1089 0.337252572 603.9433962 582 0.501969821 138.1264368 116 0.623718674 99.33908046 85 0.975714152 114 90 13 11 104 1 0 78 42 0.755122044 0 56 306.9047619
16 -0.8128551 -0.221220 1 1 1 16 99 1306.080808 1328 0.236566572 764.8888889 749 0.460894913 136.4195402 114 0.538996501 98.62068966 80 0.88238918 97 82 14 10 104 1 1 78 41 0.740077746 0 56 324.9047619
17 -0.576192291 0.136418 1 1 1 17 113 959.9911504 998 0.303112646 638.6106195 661 0.524016252 125.3924731 113 0.564766014 89.47849462 74 1.009484509 94 80 14 4 97 1 1 78 45 0.701234508 0 56 342.9047619
18 -0.558821701 0.116543 1 1 1 18 112 1438.294643 1518 0.287682072 1043.392857 1022 0.37236516 137.2111111 109 0.542040643 92.50555556 76 0.890972924 94 80 14 0 102 1 0 76 44 0.726980118 0 56 360.9047619
19 -0.815846383 -0.191149 1 1 1 19 115 1068.295652 1077 0.249309356 609.626087 608 0.456903005 135.8817204 119 0.68117099 96.73655914 80 0.903970247 106 87 12 0 102 3 0 76 45 0.713645739 0 56 378.9047619
20 -0.79329221 -0.078398 1 1 1 20 76 1126.473684 1136 0.341777289 692.0789474 651 0.490976753 136.5320513 121 0.569094532 96.60897436 73 1.023388867 116 93 13 8 106 3 0 74 35 0.779627891 0 56 396.9047619

Total number of rows: 16896

Table truncated, full table size 3443 Kbytes.




Supplementary file Size Download File type/resource
GSM104741.tif.gz 21.9 Mb (ftp)(http) TIFF

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