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Sample GSM113725 Query DataSets for GSM113725
Status Public on Jun 13, 2006
Title WCHI_F058_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 2520 15720 110 13393 12272 3231 70 75 37 100 100 0 14529 13780 3436 125 132 56 100 100 0 0.925 0.894 0.885 0.889 1.154 0.904 0.956 80 558 27727 25857 -0.113 13323 14404 12202 13655 0
1a2b1c 2700 15720 100 2621 2303 949 71 76 39 100 100 0 2979 2785 1092 127 137 58 100 100 0 0.894 0.840 0.842 0.816 1.271 0.862 0.962 80 444 5402 4890 -0.161 2550 2852 2232 2658 0
1a3b1c 2870 15720 100 2224 2092 776 67 69 22 100 100 0 3049 2921 794 128 131 37 100 100 0 0.738 0.725 0.717 0.685 1.297 0.789 0.944 80 420 5078 4818 -0.437 2157 2921 2025 2793 0
1a4b1c 3040 15720 100 3916 3671 1160 66 71 25 100 100 0 5678 5525 1744 128 130 37 100 100 0 0.694 0.668 0.665 0.667 1.201 0.683 0.958 80 407 9400 9002 -0.528 3850 5550 3605 5397 0
1a5b1c 3200 15710 110 11396 11071 3482 71 99 348 100 100 0 9520 9288 2258 124 139 184 100 100 0 1.205 1.200 1.215 1.172 1.235 1.276 0.952 80 461 20721 20164 0.269 11325 9396 11000 9164 0
1a6b1c 3370 15710 100 1500 1537 396 73 104 360 100 97 0 4103 4199 678 127 146 191 100 100 0 0.359 0.360 0.365 0.351 1.247 0.391 0.931 80 430 5403 5536 -1.478 1427 3976 1464 4072 0
1a7b1c 3550 15720 100 3783 3774 944 72 74 31 100 100 0 3757 3611 928 125 129 45 100 100 0 1.022 1.062 1.065 1.070 1.199 1.099 0.952 80 444 7343 7188 0.031 3711 3632 3702 3486 0
1a8b1c 3720 15720 100 1131 1138 294 68 72 29 100 100 0 1443 1412 316 121 131 116 100 100 0 0.804 0.829 0.823 0.817 1.225 0.874 0.893 80 420 2385 2361 -0.315 1063 1322 1070 1291 0
1a9b1c 3890 15720 100 428 454 152 67 70 22 100 100 0 702 705 182 120 123 38 100 100 0 0.620 0.662 0.672 0.640 1.428 0.762 0.819 80 409 943 972 -0.689 361 582 387 585 0
1a10b1c 4060 15720 100 1100 1096 391 68 71 26 100 100 0 1487 1454 422 119 122 37 100 100 0 0.754 0.770 0.750 0.748 1.258 0.823 0.938 80 406 2400 2363 -0.407 1032 1368 1028 1335 0
1a11b1c 4230 15720 100 3185 3025 1095 69 71 21 100 100 0 3661 3493 1215 123 126 39 100 100 0 0.881 0.877 0.878 0.867 1.282 0.899 0.953 80 418 6654 6326 -0.183 3116 3538 2956 3370 0
1a12b1c 4400 15730 100 1500 1427 504 69 73 30 100 100 0 1764 1650 596 127 132 57 100 100 0 0.874 0.892 0.897 0.904 1.311 0.903 0.939 80 420 3068 2881 -0.194 1431 1637 1358 1523 0
1a13b1c 4570 15720 100 462 457 151 68 71 23 100 98 0 729 711 187 119 123 37 100 100 0 0.646 0.657 0.665 0.622 1.532 0.739 0.866 80 418 1004 981 -0.631 394 610 389 592 0
1a14b1c 4740 15720 100 2694 2613 642 66 70 22 100 100 0 2931 2938 560 114 118 38 100 100 0 0.933 0.902 0.911 0.882 1.270 0.948 0.951 80 406 5445 5371 -0.100 2628 2817 2547 2824 0
1a15b1c 4910 15730 100 1430 1435 345 70 86 115 100 100 0 1562 1530 310 117 132 144 100 100 0 0.941 0.966 0.978 0.959 1.216 1.036 0.930 80 442 2805 2778 -0.087 1360 1445 1365 1413 0
1a16b1c 5100 15730 110 9979 9377 2966 71 84 104 100 100 0 8449 7823 2287 124 136 141 100 100 0 1.190 1.209 1.226 1.195 1.208 1.248 0.961 80 477 18233 17005 0.251 9908 8325 9306 7699 0
1a17b1c 5260 15730 100 2492 2377 697 69 71 22 100 100 0 2887 2747 850 120 123 36 100 100 0 0.876 0.879 0.894 0.899 1.307 0.891 0.956 80 404 5190 4935 -0.192 2423 2767 2308 2627 0
1a18b1c 5410 15720 90 1572 1591 716 70 75 29 100 98 0 1891 1912 640 124 130 43 100 100 0 0.850 0.851 0.859 0.730 1.844 0.952 0.935 52 339 3269 3309 -0.234 1502 1767 1521 1788 0
1a19b1c 5600 15730 100 7042 6583 1974 71 74 25 100 100 0 9424 8912 2587 119 124 43 100 100 0 0.749 0.741 0.742 0.721 1.348 0.766 0.947 80 435 16276 15305 -0.417 6971 9305 6512 8793 0
1a20b1c 5760 15730 100 15347 15221 3260 74 76 25 100 100 0 14610 14098 3088 115 121 37 100 100 0 1.054 1.083 1.073 1.086 1.189 1.118 0.951 80 404 29768 29130 0.075 15273 14495 15147 13983 0

Total number of rows: 19213

Table truncated, full table size 3222 Kbytes.




Supplementary data files not provided
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