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Sample GSM113724 Query DataSets for GSM113724
Status Public on Jun 13, 2006
Title WCHI_F057_02-02-05
Sample type RNA
 
Channel 1
Source name EXP: lin-35(n745) mRNA
Organism Caenorhabditis elegans
Characteristics lin-35(n745) mRNA
Extracted molecule polyA RNA
Label CY3
 
Channel 2
Source name REF: N2 mRNA
Organism Caenorhabditis elegans
Characteristics N2 mRNA
Extracted molecule polyA RNA
Label CY5
 
 
Description lin-35(n745) vs N2
Data processing log base 2 ratio of cy5 to cy3
 
Submission date Jun 09, 2006
Last update date Jun 13, 2006
Contact name Valerie Reinke
E-mail(s) valerie.reinke@yale.edu
Phone 203-785-5228
Organization name Yale University School of Medicine
Department Genetics
Lab Reinke lab
Street address 333 Cedar St
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platform ID GPL3860
Series (2)
GSE5069 Expression Profiling of MAP Kinase-Mediated Meiotic Progression in C. elegans
GSE5071 Promotion of oogenesis and embryogenesis in the C. elegans gonad by EFL-1/DPL-1(E2F)does not require LIN-35(pRB)

Data table header descriptions
ID_REF
X X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
Y Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
Dia diameter in µm of the feature-indicator
F635 Median median pixel intensity of feature for Cy5 channel
F635 Mean mean pixel intensity of feature for Cy5 channel
F635 SD Cy5 pixel intensity standard deviation
B635 Median median Cy5 feature background intensity
B635 Mean mean Cy5 feature background intensity
B635 SD Cy5 background pixel intensity standard deviation
% > B635+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
% > B635+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
F635 % Sat percentage of pixel saturation within feature
F532 Median median feature pixel intensity at wavelength #2 (532 nm, Cy3)
F532 Mean mean feature background intensity at wavelength #2 (532 nm, Cy3)
F532 SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
B532 Median median feature background intensity at wavelength #2 (532 nm, Cy3)
B532 Mean mean feature background intensity at wavelength #2 (532 nm, Cy3)
B532 SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
% > B532+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm, Cy3)
% > B532+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm, Cy3)r
F532 % Sat percentage of feature pixels at wavelength #2 (Cy3) that are saturated
Ratio of Medians ratio of the background subtracted median pixel intensity at the second wavelength (Cy3), to the background subtracted median pixel intensity at the first wavelength(Cy5)
Ratio of Means ratio of the arithmetic mean of the background subtracted raw pixel intensities at the second wavelength (Cy3), to the arithmetic mean of the background subtracted raw pixel intensities at the first wavelength (Cy5)
Median of Ratios median of the pixel-by-pixel ratios of pixel intensities that have had the median background intensity subtracted of wavelength 2 (Cy3) to wavelength one (Cy5)
Mean of Ratios arithmetic mean of the pixel-by-pixel ratios of the raw pixel intensities of wavelength 2 (Cy3) to wavelength 1 (Cy5)
Ratios SD standard deviation of the log of pixel intensity ratios
Rgn Ratio regression ratio is determined by computing a linear regression between the population of pixels represented by wavelength 1 and wavelength 2
Rgn R? coefficient of determination provides a measure of the level of accuracy of the fit of the linear regression curve
F Pixels number of feature pixels
B Pixels number of background pixels
Sum of Medians sum of the median of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
Sum of Means sum of the arithmetic mean of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
VALUE Log ratio
F635 Median - B635 Cy5 median feature intensity subtracted by Cy5 median background intensity
F532 Median - B532 Cy3 median feature intensity subtracted by Cy3 median background intensity
F635 Mean - B635 Cy5 mean feature intensity subtracted by Cy5 mean background intensity
F532 Mean - B532 Cy3 mean feature intensity subtracted by Cy3 mean background intensity
Flags A value of -100 means that this spot was bad. A value of -75 means that the ID for this spot is empty. A value of -50 means that this spot cannot be aligned during analysis. A value of 0 or larger than 0 means that this spot passed the flagging screen but may still fail other quality tests.

Data table
ID_REF X Y Dia F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat Ratio of Medians Ratio of Means Median of Ratios Mean of Ratios Ratios SD Rgn Ratio Rgn R? F Pixels B Pixels Sum of Medians Sum of Means VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags
1a1b1c 2370 15960 110 15890 15798 3465 83 130 605 100 100 0 14618 14397 2711 122 148 291 100 100 0 1.090 1.101 1.108 1.092 1.176 1.197 0.920 80 561 30303 29990 0.125 15807 14496 15715 14275 0
1a2b1c 2540 15950 100 2357 2407 741 86 147 688 100 91 0 2731 2790 749 126 157 330 100 100 0 0.872 0.871 0.857 0.858 1.247 0.912 0.937 80 432 4876 4985 -0.198 2271 2605 2321 2664 0
1a3b1c 2710 15950 100 2644 2538 732 82 85 28 100 100 0 3168 3099 689 125 129 42 100 100 0 0.842 0.826 0.820 0.805 1.289 0.882 0.938 80 432 5605 5430 -0.248 2562 3043 2456 2974 0
1a4b1c 2880 15940 100 3677 3405 1025 79 86 41 100 100 0 5995 5748 1341 126 131 49 100 100 0 0.613 0.592 0.604 0.575 1.285 0.628 0.945 80 428 9467 8948 -0.706 3598 5869 3326 5622 0
1a5b1c 3050 15950 100 10495 10604 2066 85 90 41 100 100 0 8684 8644 1504 129 134 50 100 100 0 1.217 1.235 1.248 1.231 1.124 1.298 0.940 80 420 18965 19034 0.283 10410 8555 10519 8515 0
1a6b1c 3220 15950 110 1920 1868 419 92 98 70 100 100 0 4064 3909 741 136 145 103 100 100 0 0.465 0.471 0.470 0.466 1.183 0.520 0.908 80 474 5756 5549 -1.104 1828 3928 1776 3773 0
1a7b1c 3390 15950 110 3788 3417 1283 94 101 77 100 100 0 4579 4195 1215 143 153 108 100 100 0 0.833 0.820 0.819 0.772 1.390 0.894 0.928 80 494 8130 7375 -0.264 3694 4436 3323 4052 0
1a8b1c 3560 15950 110 1319 1275 427 94 106 76 100 100 0 1596 1555 383 136 151 80 100 100 0 0.839 0.832 0.829 0.800 1.353 0.976 0.857 80 475 2685 2600 -0.253 1225 1460 1181 1419 0
1a9b1c 3730 15950 100 617 605 230 92 101 68 98 96 0 820 834 242 134 144 68 100 100 0 0.765 0.733 0.702 0.688 1.459 0.823 0.863 80 420 1211 1213 -0.386 525 686 513 700 0
1a10b1c 3900 15950 100 1371 1341 493 94 99 37 100 100 0 1675 1683 545 136 144 61 100 100 0 0.830 0.806 0.772 0.783 1.296 0.852 0.928 80 420 2816 2794 -0.269 1277 1539 1247 1547 0
1a11b1c 4070 15950 100 3767 3674 1159 93 94 27 100 100 0 4341 4355 1084 134 135 40 100 100 0 0.873 0.848 0.841 0.826 1.246 0.897 0.952 80 432 7881 7802 -0.195 3674 4207 3581 4221 0
1a12b1c 4240 15960 100 1828 1776 560 93 95 29 100 100 0 2080 1974 611 133 135 39 100 100 0 0.891 0.914 0.920 0.943 1.573 0.954 0.918 80 440 3682 3524 -0.166 1735 1947 1683 1841 0
1a13b1c 4420 15950 100 685 673 231 93 95 30 100 100 0 850 876 232 132 136 41 100 100 0 0.825 0.780 0.768 0.746 1.393 0.872 0.867 80 437 1310 1324 -0.278 592 718 580 744 0
1a14b1c 4590 15950 100 3104 2981 696 87 91 29 100 100 0 3214 3167 606 126 130 43 100 100 0 0.977 0.952 0.938 0.938 1.251 1.006 0.936 80 393 6105 5935 -0.034 3017 3088 2894 3041 0
1a15b1c 4750 15960 110 2246 2168 562 81 84 27 100 100 0 2242 2139 546 116 119 37 100 100 0 1.018 1.032 0.999 1.032 1.279 1.071 0.934 80 477 4291 4110 0.026 2165 2126 2087 2023 0
1a16b1c 4930 15950 100 9751 9413 2451 73 76 30 100 100 0 9618 8963 2127 104 109 36 100 100 0 1.017 1.054 1.064 1.042 1.154 1.079 0.975 80 430 19192 18199 0.025 9678 9514 9340 8859 0
1a17b1c 5090 15950 90 2939 2840 543 66 72 52 100 100 0 2719 2701 426 94 99 39 100 100 0 1.094 1.064 1.070 1.056 1.168 1.116 0.950 52 340 5498 5381 0.130 2873 2625 2774 2607 0
1a18b1c 5260 15950 80 2265 1971 813 64 66 24 100 100 0 2168 1975 652 95 99 36 100 100 0 1.062 1.014 1.006 0.882 1.710 1.089 0.945 52 302 4274 3787 0.086 2201 2073 1907 1880 0
1a19b1c 5430 15950 90 8912 8683 1484 63 99 373 100 100 0 8672 8496 1147 99 121 224 100 100 0 1.032 1.027 1.035 1.020 1.117 1.081 0.948 52 369 17422 17017 0.046 8849 8573 8620 8397 0
1a20b1c 5610 15960 100 12179 11056 2627 64 83 282 100 100 0 12402 11396 3095 94 111 202 100 100 0 0.984 0.973 0.958 1.015 1.481 0.991 0.947 80 442 24423 22294 -0.023 12115 12308 10992 11302 0

Total number of rows: 19213

Table truncated, full table size 3251 Kbytes.




Supplementary data files not provided
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