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Sample GSM543838 Query DataSets for GSM543838
Status Public on Dec 06, 2010
Title Ymr1 IP (3) A
Sample type RNA
 
Channel 1
Source name Extract tot. RNA Ymr1-TAP (3)
Organism Saccharomyces cerevisiae
Characteristics experiment: Extract tot. RNA Ymr1-TAP (3)
Growth protocol yeast cells expressing TAP-tagged RBP or the wild-type strain BY4741 (mock control) were grown to mid-log phase in rich medium and harvested by centrifugation.
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Affinity isolated RNA, Ymr1-TAP (3)
Organism Saccharomyces cerevisiae
Characteristics experiment: Affinity isolated RNA, Ymr1-TAP (3)
Growth protocol yeast cells expressing TAP-tagged RBP or the wild-type strain BY4741 (mock control) were grown to mid-log phase in rich medium and harvested by centrifugation.
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol GenePix 4200A
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72322.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date May 17, 2010
Last update date Dec 06, 2010
Contact name Andre Gerber
E-mail(s) [email protected]
Phone +41 44 6337378
Fax +41 44 6337364
Organization name Swiss Federal Institute of Technology
Department Institute of Pharmaceutical Science
Street address Wolfgang Pauli Str. 10, HCI H396
City ETH Hoenggerberg, Zuerich
ZIP/Postal code ZH
Country Switzerland
 
Platform ID GPL8306
Series (1)
GSE21864 RNA-affinity isolations 13 RBPs

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 1633 248 64 91 1569 157 1735 261 65 92 1671 170 0 0 1052 107 11 16 96 88 94 80 1726 1841 9.994 .1 .102 .121 .103 2.35 52 340 .098 .97 80 1990 7140 46 54 79 87 0 2920 1071 1848 1.178 3073 2001 .849 1.198 .236 .26
2 629 138 66 94 563 44 612 135 67 94 546 41 0 0 145 20 10 16 100 96 100 62 607 587 12.795 .078 .075 .072 .076 1.537 32 176 .08 .76 60 2200 7150 48 54 101 107 0 1625 1107 518 .92 1589 483 1.087 .884 -.12 -.178
3 1801 252 63 92 1738 160 1817 246 64 90 1754 154 0 0 577 66 12 17 100 100 100 100 1898 1908 10.863 .092 .088 .089 .091 1.346 32 176 .092 .94 60 2420 7150 48 54 123 129 0 2967 1083 1884 1.084 2896 1813 .923 1.034 .116 .048
4 256 131 64 90 192 41 261 128 66 92 197 38 0 0 59 28 30 18 100 71 100 53 233 235 4.683 .214 .193 .158 .186 2.438 32 176 .214 .71 60 2640 7150 48 54 145 151 0 1542 1060 483 2.514 1507 447 .398 2.271 1.33 1.183
5 256 114 65 91 191 23 267 114 66 92 202 23 0 0 75 23 11 16 100 59 96 21 214 225 8.304 .12 .114 .116 .118 2.842 32 176 .11 .48 60 2870 7150 48 54 168 174 0 1342 1071 271 1.418 1342 271 .705 1.341 .504 .423
6 306 140 62 91 244 49 318 142 63 91 256 51 0 0 84 32 9 16 100 81 100 71 293 307 4.98 .201 .199 .189 .216 1.782 32 176 .205 .74 60 3090 7140 47 53 190 196 0 1648 1071 577 2.364 1672 600 .423 2.345 1.241 1.23
7 874 141 64 90 810 51 837 138 64 89 773 48 0 0 225 33 11 14 100 93 100 75 861 821 15.882 .063 .062 .061 .07 1.733 32 236 .067 .77 70 3310 7150 47 54 211 218 0 1660 1060 600 .741 1625 565 1.349 .731 -.432 -.452
8 802 135 61 89 741 46 842 129 63 89 781 40 0 0 287 26 10 14 100 90 100 71 787 821 16.109 .062 .051 .054 .057 1.963 32 236 .054 .72 70 3520 7150 47 54 232 239 0 1589 1048 542 .731 1519 471 1.368 .603 -.452 -.73
9 416 122 62 90 354 32 419 116 63 91 357 26 0 0 111 25 9 16 100 75 100 40 386 383 11.063 .09 .073 .08 .07 1.98 32 176 .087 .6 60 3750 7150 48 54 256 262 0 1436 1060 377 1.064 1366 306 .94 .857 .09 -.222
10 635 128 63 89 572 39 630 130 66 92 567 41 0 0 177 26 41 24 100 75 100 31 611 608 14.667 .068 .072 .058 .065 2.304 32 236 .066 .65 70 3970 7150 47 54 277 284 0 1507 1048 459 .803 1531 483 1.246 .851 -.317 -.232
11 2159 184 63 89 2096 95 2076 178 64 90 2013 89 0 0 661 38 12 16 100 96 100 96 2191 2102 22.063 .045 .044 .045 .044 1.292 32 236 .045 .91 70 4190 7150 47 54 299 306 0 2166 1048 1118 .534 2096 1048 1.874 .521 -.906 -.942
12 174 109 61 90 113 19 172 109 61 90 111 19 0 0 37 18 10 16 100 53 100 21 132 130 5.947 .168 .171 .189 .241 2.211 32 236 .167 .4 70 4410 7150 47 54 321 328 0 1283 1060 224 1.98 1283 224 .505 2.015 .985 1.011
13 540 122 60 90 480 32 534 121 61 90 474 31 0 0 146 24 10 15 100 75 100 50 512 505 15 .067 .065 .062 .07 2.103 32 236 .059 .57 70 4630 7150 47 54 343 350 0 1436 1060 377 .785 1425 365 1.274 .77 -.349 -.377
14 852 117 61 90 791 27 791 109 61 89 730 19 0 0 257 27 9 16 100 53 100 31 818 749 29.296 .034 .026 .022 .028 3.109 32 236 .034 .54 70 4850 7150 47 54 365 372 0 1377 1060 318 .402 1283 224 2.488 .306 -1.315 -1.706
15 761 136 59 89 702 47 779 132 61 89 720 43 0 0 228 30 10 15 100 84 100 65 749 763 14.936 .067 .06 .056 .059 2.13 32 176 .064 .71 60 5060 7150 48 54 387 393 0 1601 1048 553 .788 1554 506 1.269 .703 -.343 -.508
16 3787 277 62 88 3725 189 3654 263 62 88 3592 175 0 0 955 68 10 16 100 100 100 100 3914 3767 19.709 .051 .049 .049 .05 1.288 32 236 .051 .95 70 5290 7160 48 55 409 416 0 3261 1036 2225 .597 3096 2060 1.674 .574 -.743 -.802
17 982 261 59 92 923 169 910 244 61 93 851 152 0 0 307 71 11 17 100 100 100 100 1092 1003 5.462 .183 .179 .177 .168 1.368 32 236 .175 .93 70 5510 7160 48 55 431 438 0 3073 1083 1990 2.156 2873 1790 .464 2.103 1.108 1.072
18 507 148 61 88 446 60 492 147 61 89 431 59 0 0 130 32 9 15 100 93 100 78 506 490 7.433 .135 .137 .121 .134 1.83 32 236 .133 .78 70 5730 7160 48 55 453 460 0 1742 1036 706 1.584 1731 695 .631 1.612 .663 .689
19 727 131 63 91 664 40 673 127 65 93 610 36 0 0 218 32 15 17 100 75 100 50 704 646 16.6 .06 .059 .045 .057 2.862 32 176 .067 .75 60 5950 7150 48 54 476 482 0 1542 1071 471 .709 1495 424 1.41 .695 -.496 -.525
20 132 109 67 91 65 18 135 107 66 92 68 16 0 0 25 22 10 16 93 50 93 25 83 84 3.611 .277 .235 .279 .343 2.432 32 236 .252 .3 70 1990 7370 69 76 79 86 0 1283 1071 212 3.26 1260 188 .307 2.77 1.705 1.47

Total number of rows: 10944

Table truncated, full table size 2314 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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