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Sample GSM124979 Query DataSets for GSM124979
Status Public on Sep 30, 2006
Title VREI_F041_11-02-04
Sample type RNA
 
Channel 1
Source name REF
Organism Caenorhabditis elegans
Characteristics N2 mRNA
Extracted molecule polyA RNA
Label CY3
 
Channel 2
Source name EXP
Organism Caenorhabditis elegans
Characteristics mes-4(bn85) mRNA
Extracted molecule polyA RNA
Label CY5
 
 
Description mes-4(bn85) vs N2 #4
Data processing log base 2 ratio of cy5 to cy3
 
Submission date Aug 03, 2006
Last update date Aug 07, 2006
Contact name Valerie Reinke
E-mail(s) [email protected]
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
GSE5454 MES-4, an autosome-associated HMT that participates in silencing the X chromosomes in the C. elegans germ line

Data table header descriptions
ID_REF
ID3 Accession Number
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 �m 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 ID3 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 C53H9.2::+ 2660 15520 110 30574 30346 6513 179 183 62 100 100 0 27830 27742 4887 219 224 67 100 100 0 1.101 1.096 1.09 1.083 1.178 1.112 0.96 80 535 58006 57690 0.139 30395 27611 30167 27523 0
1a2b1c C55C2.4::+ 2830 15510 110 6833 6735 2402 190 194 60 100 100 0 5040 5451 1873 228 231 51 100 100 0 1.381 1.253 1.266 1.243 1.172 1.28 0.973 80 462 11455 11768 0.465 6643 4812 6545 5223 0
1a3b1c W03D8.2::+ 3000 15510 110 7642 6892 2440 190 196 63 100 100 0 5652 5752 1653 231 237 54 100 100 0 1.375 1.214 1.238 1.112 1.476 1.269 0.963 80 462 12873 12223 0.459 7452 5421 6702 5521 0
1a4b1c K09H9.3::+ 3170 15510 110 11756 10963 3598 194 207 103 100 100 0 11133 10821 2719 234 243 100 100 100 0 1.061 1.017 1.022 0.942 1.426 1.069 0.962 80 411 22461 21356 0.085 11562 10899 10769 10587 0
1a5b1c M01D7.6::+ 3330 15510 120 15562 13109 7794 192 203 97 96 91 0 13761 11863 6443 231 238 96 98 93 0 1.136 1.11 1.114 0.959 1.801 1.174 0.949 120 484 28900 24549 0.184 15370 13530 12917 11632 0
1a6b1c C55C2.2::+ 3500 15510 100 8006 7772 2031 203 212 79 100 100 0 8184 8004 2021 229 234 76 100 100 0 0.981 0.974 0.978 0.97 1.14 1.01 0.961 80 372 15758 15344 -0.028 7803 7955 7569 7775 0
1a7b1c F32B5.8::+ 3670 15520 110 7457 7159 2125 195 202 76 100 100 0 5945 5674 1717 231 236 72 100 100 0 1.271 1.279 1.253 1.299 1.21 1.29 0.947 80 461 12976 12407 0.346 7262 5714 6964 5443 0
1a8b1c K09H9.1::+ 3840 15520 110 3373 3302 967 188 193 60 100 100 0 2835 2654 806 229 231 53 100 100 0 1.222 1.284 1.273 1.31 1.257 1.292 0.931 80 462 5791 5539 0.289 3185 2606 3114 2425 0
1a9b1c M01D7.4::nb 4010 15510 100 1011 995 364 184 188 58 98 96 0 1011 985 305 229 229 48 98 97 0 1.058 1.073 1.05 1.04 1.367 1.16 0.877 80 392 1609 1567 0.081 827 782 811 756 0
1a10b1c T16H5.1::+ 4180 15510 110 3159 3125 1106 195 200 80 100 100 0 2780 2748 816 230 239 65 100 100 0 1.162 1.164 1.164 1.113 1.32 1.221 0.962 80 461 5514 5448 0.217 2964 2550 2930 2518 0
1a11b1c F32B5.6::+ 4350 15510 110 5764 5623 1950 190 196 66 100 100 0 5038 4952 1449 223 232 58 100 100 0 1.158 1.149 1.15 1.096 1.316 1.203 0.963 80 424 10389 10162 0.211 5574 4815 5433 4729 0
1a12b1c C45E1.3::+ 4510 15520 120 3377 3062 2136 182 212 335 77 73 0 2985 2663 1749 223 242 205 83 75 0 1.157 1.18 1.17 1.085 1.556 1.255 0.943 120 501 5957 5320 0.21 3195 2762 2880 2440 0
1a13b1c M01D7.2::nb 4690 15510 100 1215 1085 404 184 203 295 91 77 0 1142 1095 328 218 235 205 97 90 0 1.116 1.027 0.993 0.971 1.452 1.121 0.915 80 401 1955 1778 0.158 1031 924 901 877 0
1a14b1c F23C8.11::+ 4860 15510 110 5612 5102 2087 174 181 58 100 100 0 4672 4513 1414 216 220 50 100 100 0 1.22 1.147 1.172 1.003 1.642 1.235 0.964 80 447 9894 9225 0.287 5438 4456 4928 4297 0
1a15b1c F32B5.3::+ 5030 15520 110 5139 5207 1234 172 178 59 100 100 0 4549 4471 881 212 214 48 100 100 0 1.145 1.182 1.169 1.167 1.18 1.219 0.965 80 448 9304 9294 0.196 4967 4337 5035 4259 0
1a16b1c M01B12.5::+ 5190 15510 100 5494 5122 2179 171 181 71 98 98 0 5189 4720 1790 213 218 60 100 100 0 1.07 1.099 1.096 1.006 1.465 1.149 0.97 80 380 10299 9458 0.097 5323 4976 4951 4507 0
1a17b1c F47G6.4::+ 5360 15510 100 4953 4369 1826 171 179 72 97 95 0 4446 3915 1639 209 213 58 98 97 0 1.129 1.133 1.118 1.077 1.39 1.15 0.971 80 418 9019 7904 0.175 4782 4237 4198 3706 0
1a18b1c F23C8.8::+ 5530 15520 90 3858 3587 1047 178 183 57 100 100 0 3335 3076 902 212 216 52 100 100 0 1.178 1.19 1.188 1.205 1.196 1.205 0.963 52 354 6803 6273 0.237 3680 3123 3409 2864 0
1a19b1c F32B5.1::+ 5710 15520 110 10016 9430 3181 174 176 53 100 100 0 10794 10093 2655 207 211 51 100 100 0 0.93 0.936 0.942 0.873 1.489 0.982 0.963 80 472 20429 19142 -0.105 9842 10587 9256 9886 0
1a20b1c M01B12.3::+ 5870 15520 110 8769 8612 3082 165 173 53 100 100 0 8133 8038 2204 210 213 49 100 100 0 1.086 1.079 1.082 1.003 1.551 1.142 0.958 80 475 16527 16275 0.119 8604 7923 8447 7828 0

Total number of rows: 19213

Table truncated, full table size 3599 Kbytes.




Supplementary data files not provided
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