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Sample GSM104739 Query DataSets for GSM104739
Status Public on Apr 30, 2006
Title CGH_replicate2
Sample type genomic
 
Channel 1
Source name genomic DNA, D. rerio
Organism Danio rerio
Characteristics Organism: D. 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: P. moluccensis
Tissue: caudal fin
sample ID: LJ50
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 -0.426814667 -0.017516 1 1 1 1 98 1194.295918 1242 0.377950145 902.9795918 915 0.503379573 134.922619 71 0.844187438 147.5 93 1.301257318 67 88 12 0 62 0 0 95 40 0.7696902 0 60 57.9047619
2 -0.149292418 0.008790 1 1 1 2 109 5708.201835 5861 0.249682351 5196.633028 5274 0.322496754 295.4770115 75 0.920204631 410.4885057 132 1.292768303 69 100 12 12 65 0 0 95 42 0.776493422 0 60 75.9047619
3 -0.295972974 0.108263 1 1 1 3 98 2355.673469 2422 0.305003659 1952.94898 1963 0.369814447 137.8218391 70 0.771618796 149.4770115 89 1.485823956 69 100 12 2 65 0 0 89 41 0.732602213 0 60 94.9047619
4 -0.198727668 0.102031 1 1 1 4 124 3664.08871 3781 0.17226243 3229.032258 3284 0.347186246 162.9252874 73 0.607787332 193.0574713 107 1.23884163 71 103 12 2 65 0 0 89 48 0.676315085 0 60 112.9047619
5 -0.867425841 -0.409451 1 1 1 5 107 1247.88785 1237 0.23338899 730.1775701 672 0.570461881 181.1776316 69 0.867100488 171.0789474 103 1.356441398 69 112 11 2 59 0 0 98 42 0.762245837 0 60 130.9047619
6 -0.68740977 -0.147131 1 1 1 6 110 748.2272727 755 0.268714986 506.4545455 462 0.549728422 122.5314286 72 0.741003202 143.3085714 116 1.355835154 69 113 11 9 60 0 0 98 44 0.71399833 0 60 147.9047619
7 -0.70519126 -0.291507 1 1 1 7 121 2340.619835 2407 0.227317338 1479.561983 1469 0.426278404 217.2944444 81 0.736822244 197.8833333 107 1.518466134 73 97 12 9 60 0 0 98 43 0.82235308 0 60 164.9047619
8 -0.68795467 -0.232405 1 1 1 8 119 790.2941176 803 0.3454678 505.8991597 491 0.642946527 94.42487047 63 0.796331417 113.7564767 91 1.147064672 69 97 12 9 60 0 0 98 47 0.676957041 0 60 182.9047619
9 -0.692427198 -0.286226 1 1 1 9 111 1615.225225 1628 0.273433477 1017.378378 1000 0.454810982 187.1485714 72 0.877070019 190.1428571 114 1.437828011 68 113 12 9 67 0 0 91 44 0.720489224 0 60 200.9047619
10 -0.941766734 -0.561688 1 1 1 10 115 891.1217391 886 0.345950981 461.5652174 455 0.594918636 100.0289017 73 0.815749503 129.0289017 106 1.293584963 71 113 12 4 67 0 0 98 47 0.654202182 0 60 218.9047619
11 -0.325890061 -0.063768 1 1 1 11 117 3894.119658 4022 0.240100177 3088.948718 3200 0.3558268 157.1944444 76 0.790139447 177.7777778 109 1.230539832 67 118 11 4 67 0 0 98 44 0.759434588 0 60 236.9047619
12 -0.62898444 -0.139639 1 1 1 12 116 1461.405172 1525 0.39652489 1012.732759 979 0.577000736 107.1546961 70 0.673729095 123.6077348 100 1.073133203 64 112 11 6 67 0 0 94 45 0.719851354 0 60 253.9047619
13 -0.503110747 -0.094518 1 1 1 13 92 612.826087 602 0.464542687 424.0869565 417 0.494773915 90.37426901 69 0.604419065 108.374269 84 1.046987923 69 107 11 6 63 0 0 85 43 0.625260193 0 60 270.9047619
14 -0.26517666 0.154432 1 1 1 14 103 2468.786408 2573 0.438712851 2126.271845 2131 0.42258205 99.64367816 67 0.723918839 132.4482759 96 1.285650835 66 107 12 10 63 0 0 86 42 0.733750665 0 60 288.9047619
15 -0.622066495 -0.159097 1 1 1 15 100 822.06 782 0.487703206 549.28 499 0.531686212 89.51111111 66 0.682675881 106.7555556 89 1.13345902 70 84 14 11 63 0 0 86 43 0.679630644 0 60 307.9047619
16 -0.463692004 -0.002423 1 1 1 16 100 971.74 989 0.28383762 727.23 707 0.46039477 91.11494253 66 0.63372376 107.908046 85 1.180442307 70 86 14 11 61 0 0 98 41 0.747553279 0 60 326.9047619
17 -0.118158368 0.326357 1 1 1 17 92 785.1521739 777 0.374595174 714.0108696 703 0.570014495 85.44047619 64 0.576613364 126.5 101 1.123930097 56 100 14 13 64 0 0 98 39 0.760096053 0 60 344.9047619
18 -0.284906873 0.223757 1 1 1 18 99 1158.545455 1196 0.272822958 1020.10101 971 0.4367372 103.7028571 70 0.702903356 130.2571429 97 1.061571017 61 115 13 10 64 0 0 98 43 0.672834338 0 60 361.9047619
19 -0.635192837 -0.159344 1 1 1 19 109 730.7155963 729 0.386266325 489.1743119 461 0.572519193 89.56111111 70 0.631271777 116.8388889 94 1.161924568 61 132 13 10 64 0 0 82 44 0.707507436 0 60 380.9047619
20 -0.359373324 0.053723 1 1 1 20 70 691.1285714 655 0.513927604 532.0714286 502 0.858661619 77.4522293 65 0.594707108 122.7197452 100 1.249843258 61 75 11 5 61 0 0 83 36 0.678739154 0 60 397.9047619

Total number of rows: 16896

Table truncated, full table size 3378 Kbytes.




Supplementary file Size Download File type/resource
GSM104739.tif.gz 20.4 Mb (ftp)(http) TIFF

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