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Sample GSM38424 Query DataSets for GSM38424
Status Public on Sep 04, 2005
Title Muvar_59b51b
Sample type RNA
 
Channel 1
Source name Mutation accumulation line 59, late 3rd instar larvae (blue gut)
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Channel 2
Source name Mutation accumulation line 51, late 3rd instar larvae (blue gut)
Organism Drosophila melanogaster
Extracted molecule total RNA
 
 
Description Comparison between mutation accumulation lines 59 at the late 3rd instar larvae (blue gut) and 51 at the late 3rd instar larvae (blue gut).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0. http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster
 
Submission date Jan 04, 2005
Last update date Aug 01, 2005
Contact name Scott A Rifkin
Phone 617-496-5540
URL http://kim.bio.upenn.edu/~scott/
Organization name Harvard University
Department OEB
Lab Hartl Lab
Street address 16 Divinity Ave
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platform ID GPL1784
Series (1)
GSE2126 Drosophila melanogaster mutation accumulation lines

Data table header descriptions
ID_REF
BLOCK block on the array (see platform description)
ROW row in the block (max = 25)
COLUMN column in the block (max = 25)
AREA The number of pixels in the segmented spot
CH1_MEAN The average pixel value within the spot for sample 1
CH1_MEDIAN The average pixel value within the spot for sample 1
CH1_IQR The interquartile range of the logged pixel values within the spot for sample 1
CH1_BGMEAN The average pixel value in the background region for sample 1
CH1_BGMEDIAN The median pixel value in the background region for sample 1
CH1_BGSD The interquartile range of the logged pixel values in the background region for sample 1
CH1_VALLEY Median of median image values in four neighbouring valley regions for sample 1: Valley regions are square regions between spots
CH1_MORPH Value of a morphological opening of sample 1 at the nominal spot centre. Openings and erosions use a rectangular structuring element with side lengths equal to twice the average horizontal and vertical distances between spots
CH1_MORPH_ERODE Value of a morphological erosion of sample 1 at the nominal spot centre
CH1_MORPH_CLOSE_OPEN Value of a morphological closing followed by a morphological opening of sample 1 at the nominal spot centre
CH1_TRANSFORMED Log-2 value for sample 1 for a spot after sample and series normalizations. This is the value used in the subsequent analyses
CH2_MEAN The average pixel value within the spot for sample 2
CH2_MEDIAN The average pixel value within the spot for sample 2
CH2_IQR The interquartile range of the logged pixel values within the spot for sample 2
CH2_BGMEAN The average pixel value in the background region for sample 2
CH2_BGMEDIAN The median pixel value in the background region for sample 2
CH2_BGSD The interquartile range of the logged pixel values in the background region for sample 2
CH2_VALLEY Median of median image values in four neighbouring valley regions for sample 2: Valley regions are square regions between spots
CH2_MORPH Value of a morphological opening of sample 2 at the nominal spot centre. Openings and erosions use a rectangular structuring element with side lengths equal to twice the average horizontal and vertical distances between spots
CH2_MORPH_ERODE Value of a morphological erosion of sample 2 at the nominal spot centre
CH2_MORPH_CLOSE_OPEN Value of a morphological closing followed by a morphological opening of sample 2 at the nominal spot centre
CH2_TRANSFORMED Log-2 value for sample 2 for a spot after sample and series normalizations. This is the value used in the subsequent analyses
VALUE The base-2 log of the background-adjusted ratio, R/G, using R/Gmedian for spot value and morphR/G for background. Note that this value is NOT used in the subsequent analyses (see CH1&CH2_TRANSFORMED)
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</tt> times four pi divided by perimeter squared. This is ideally one for circles and more than one for other shapes
FLAG A flag which is one if the spot area is greater than the product of the horizontal and vertical average spot separations, or if the spot is flagged by visual inspection, or flagged in the platform

Data table
ID_REF BLOCK ROW COLUMN AREA CH1_MEAN CH1_MEDIAN CH1_IQR CH1_BGMEAN CH1_BGMEDIAN CH1_BGSD CH1_VALLEY CH1_MORPH CH1_MORPH_ERODE CH1_MORPH_CLOSE_OPEN CH1_TRANSFORMED CH2_MEAN CH2_MEDIAN CH2_IQR CH2_BGMEAN CH2_BGMEDIAN CH2_BGSD CH2_VALLEY CH2_MORPH CH2_MORPH_ERODE CH2_MORPH_CLOSE_OPEN CH2_TRANSFORMED VALUE PERIMETER CIRCULARITY FLAG
0 1 1 1 89 1227.91011235955 1396 0.246009376051213 224.378205128205 109 0.457137118652485 88 40 33 93 12.7045846224 1254.96629213483 1435 0.24384286732736 225.557692307692 86 0.661398482245366 73 25 21 80 12.7183102598 0.0563379841498128 36 0.862968352374974 1
1 1 1 2 84 1376.57142857143 1576 0.190238114871806 230.102564102564 108 0.562932540561417 103 35 31 99 12.7495367634 1499.96428571429 1711 0.272753831329959 238.141025641026 95 0.795426029680364 72 25 21 83 12.781144786 0.129737674427298 36 0.81448698426402 1
2 1 1 3 81 1426.65432098765 1585 0.187092058598062 270.147435897436 112 0.714887167196352 103 41 31 99 12.7502203633 1630.02469135802 1796 0.255200443533857 275.916666666667 104 0.867218837881758 72 25 22 83 12.7984327099 0.197891459483834 36 0.785398163397448 1
3 1 1 4 76 1115.34210526316 1267 0.208989803876116 298.927152317881 123 0.830618171188548 96 41 33 99 12.6691612221 1116.75 1283 0.273801129658438 280.807947019868 95 1.02850272248108 74 25 22 83 12.6782176757 0.0371729431885067 35 0.779627891176569 1
4 1 1 5 79 1319.29113924051 1469 0.22551228514976 312.066666666667 131 1.03777062941186 95 41 33 99 12.7227688924 1497.82278481013 1678 0.275981821976116 299.933333333333 104 1.11646990606812 74 27 22 83 12.7737714587 0.209344140884159 34 0.858774462399978 1
5 1 1 6 66 1504.30303030303 1613 0.157614886524928 341.053333333333 116 0.920629133472753 90 44 33 96 12.7558659097 1802.57575757576 1930 0.150755090826120 342.44 95 1.01780825625281 74 27 20 78 12.8236999323 0.278430209305924 34 0.717457145802513 1
6 1 1 7 68 1494.22058823529 1597 0.180589954629676 337.335526315789 113 1.08280168264147 90 44 36 97 12.7522632218 1745.95588235294 1886 0.183488418069875 348.203947368421 88 1.13335523711198 71 27 20 78 12.8154777057 0.259468940532181 34 0.739198271432893 1
7 1 1 8 81 2416.95061728395 1488 0.254060503978937 918.423076923077 113 1.11696142733631 94 44 36 97 12.726685191 2786.12345679012 1752 0.225103695685684 1256.76282051282 101 1.30058084284586 70 26 22 78 12.7893862928 0.257361722291784 36 0.785398163397448 1
8 1 1 9 82 1261.34146341463 1383 0.197202185287641 300.293333333333 110 0.864997437486604 94 44 34 96 12.7001502551 1440 1588 0.279063805951906 290.373333333333 92 1.16220339144964 79 26 22 78 12.7542942755 0.222238492817670 34 0.891386150845547 1
9 1 1 10 83 1242.63855421687 1364 0.168566181725469 253.905063291139 113 0.59550871099603 101 44 34 94 12.6951270789 1477.12048192771 1644 0.229466017053697 237.031645569620 92 0.603535021870258 75 26 22 78 12.7666748718 0.293673678184161 36 0.80479071064183 1
10 1 1 11 74 1280.90540540541 1372 0.172930574478855 287.019867549669 106 0.973178106276206 93 44 33 93 12.6972508567 1541.47297297297 1651 0.27782977600877 284.900662251656 93 1.01024313821802 66 26 21 77 12.7681922279 0.291184571456255 35 0.759111367724554 1
11 1 1 12 82 1291.03658536585 1385 0.163032631522388 240.365384615385 100 0.566395474920801 92 44 29 92 12.7006748584 1484.76829268293 1640 0.233998666010326 227.903846153846 85 0.685425134466035 68 24 21 77 12.7662401356 0.269117960847321 36 0.795094437019639 1
12 1 1 13 89 1207.08988764045 1292 0.220829765463940 232.564102564103 105 0.744734549350438 91 38 29 93 12.6770982985 1413.85393258427 1499 0.317447911650162 202.326923076923 92 0.742627237823315 74 24 13 75 12.7341510482 0.234177606334526 36 0.862968352374974 1
13 1 1 14 90 1222.78888888889 1344 0.219701207123237 198.471337579618 101 0.474457979595116 87 37 31 96 12.6916483341 1436.96666666667 1619 0.228664125884154 160.152866242038 84 0.6458942957094 74 24 13 75 12.7616426441 0.287297282856799 37 0.826131011900895 1
14 1 1 15 91 1198.23076923077 1278 0.179597345488423 198.955128205128 103 0.462623521948113 88 39 31 96 12.6728685945 1382.62637362637 1495 0.283060342131127 175.205128205128 87 0.58279912339108 72 28 13 75 12.7322395049 0.243692683532788 36 0.882360899619355 1
15 1 1 16 84 1188.42857142857 1264 0.137817725805208 180.240740740741 101 0.448693842658984 89 42 39 96 12.66801258 1396.23809523810 1506 0.230005949575251 171.179012345679 84 0.534082485930258 69 28 26 75 12.7348652052 0.274401984327421 38 0.731007708868539 1
16 1 1 17 86 1224.72093023256 1314 0.175863581240007 197.333333333333 111 0.614556905966724 93 42 39 96 12.6821076587 1379.55813953488 1535 0.222399780361365 186.543209876543 87 0.686080013336853 71 26 26 75 12.7421610875 0.246494135242328 38 0.74841265431779 1
17 1 1 18 86 1173.53488372093 1233 0.182174183718748 198.705128205128 105 0.618111994617031 94 42 41 93 12.6589809941 1475.59302325581 1604 0.253371449617582 183.903846153846 89 0.640304699185565 71 26 24 75 12.7578763107 0.405923792149344 36 0.833879531508402 1
18 1 1 19 83 1217.61445783133 1299 0.210310466696187 186.496815286624 111 0.570014495156321 97 44 41 93 12.6773784771 1461.25301204819 1551 0.221812288637012 167.993630573248 89 0.591097926205776 77 24 16 83 12.7463289327 0.283012697958718 37 0.761876377641937 1
19 1 1 20 86 1216.37209302326 1274 0.173449416566566 178.687116564417 106 0.45953232937844 96 44 39 97 12.6703061227 1502.15116279070 1570 0.246383730824266 172.975460122699 90 0.608806032126195 73 24 16 83 12.7506753591 0.329882003698245 38 0.74841265431779 1

Total number of rows: 20000

Table truncated, full table size 5072 Kbytes.




Supplementary data files not provided
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