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Sample GSM259467 Query DataSets for GSM259467
Status Public on Aug 26, 2008
Title Khd1 IP (2)
Sample type RNA
 
Channel 1
Source name tot. RNA Khd1 extract (2)
Organism Saccharomyces cerevisiae
Characteristics tot. RNA Khd1 extract (2)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Khd1 IP RNA (2)
Organism Saccharomyces cerevisiae
Characteristics Khd1 IP RNA (2)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol Gerber et al. (2004) PLoS Biology; The protocol can be found in the Series supplementary file
 
 
Hybridization protocol not provided
Scan protocol Scanner Make = Axon Instruments (V1.00); Scanner Model = GenePix 4000B [81971]; Scanning software = AxImageIO
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/30144.gif
Strain Name: tagged
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 Jan 25, 2008
Last update date Aug 26, 2008
Contact name Andre Gerber
E-mail(s) andre.gerber@pharma.ethz.ch
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 GPL6421
Series (1)
GSE10279 Khd1p associated mRNAs

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
1 628 1082 79 79 549 1003 565 1061 81 85 486 982 0 0 220 355 17 30 100 100 100 100 1552 1468 .547 1.827 2.021 1.864 1.901 1.263 80 495 1.838 .96 110 1090 18220 44 55 27 38 0 784 57 727 1.324 769 712 .755 1.464 .405 .55
2 88 90 77 77 11 13 81 76 79 80 4 -1 0 0 28 50 15 20 21 20 11 11 24 3 .846 1.182 null 1.263 1.222 2.893 80 411 1.541 .59 100 1270 18200 43 53 46 56 -50 65 56 9 .856 55 null 1.168 null -.224 null
3 18970 11147 76 72 18894 11075 14935 8624 77 76 14859 8552 0 0 12482 7437 15 20 100 100 100 100 29969 23411 1.706 .586 .576 .576 .57 1.313 120 535 .582 .97 130 1440 18220 43 56 61 74 0 8078 52 8025 .425 6249 6197 2.354 .417 -1.235 -1.262
4 1510 2006 76 71 1434 1935 1525 1855 77 74 1449 1784 0 0 736 968 15 17 100 100 100 100 3369 3233 .741 1.349 1.231 1.374 1.378 1.222 120 581 1.349 .98 130 1620 18220 43 56 79 92 0 1454 51 1402 .978 1344 1293 1.023 .892 -.032 -.165
5 90 84 75 69 15 15 76 71 75 71 1 2 0 0 42 38 13 14 27 30 15 22 30 3 1 1 2 1.247 1.2 2.821 80 417 1.133 .65 100 1800 18200 43 53 99 109 -50 61 50 11 .725 51 1 1.38 1.449 -.465 .535
6 94 89 76 68 18 21 81 75 77 71 5 7 0 0 47 48 13 16 31 33 20 16 39 12 .857 1.167 1.4 .909 .896 3.232 80 411 1.203 .7 100 1970 18200 43 53 116 126 -50 64 49 15 .845 54 5 1.183 1.014 -.242 .021
7 1030 1384 76 70 954 1314 1060 1411 77 73 984 1341 0 0 463 577 13 17 100 100 100 100 2268 2325 .726 1.377 1.363 1.434 1.447 1.296 120 556 1.354 .97 130 2150 18220 43 56 132 145 0 1003 51 952 .998 1022 972 1.002 .988 -.003 -.018
8 1735 2649 76 67 1659 2582 1790 2476 76 68 1714 2409 0 0 978 1714 12 13 100 100 100 100 4241 4123 .643 1.556 1.405 1.437 1.692 1.64 120 471 1.658 .95 120 2340 18210 43 55 152 164 0 1920 49 1871 1.128 1794 1746 .887 1.018 .174 .026
9 472 676 76 66 396 610 474 676 77 67 398 610 0 0 200 252 13 12 100 100 100 100 1006 1008 .649 1.54 1.533 1.625 1.608 1.293 120 532 1.499 .96 130 2500 18210 42 55 167 180 0 490 48 442 1.116 490 442 .896 1.111 .159 .151
10 750 950 80 66 670 884 756 972 81 67 676 906 0 0 321 386 14 12 100 100 100 100 1554 1582 .758 1.319 1.34 1.32 1.446 1.514 80 417 1.33 .9 100 2680 18210 44 54 187 197 0 688 48 641 .956 704 657 1.046 .971 -.065 -.042
11 978 1182 80 68 898 1114 1011 1020 80 69 931 952 0 0 544 673 13 13 100 100 100 100 2012 1883 .806 1.241 1.023 1.235 1.307 1.45 120 557 1.251 .96 120 2860 18200 42 54 204 216 0 857 49 807 .899 739 690 1.112 .741 -.154 -.432
12 1571 3317 79 70 1492 3247 1609 3559 81 71 1530 3489 0 0 657 1351 13 14 100 100 100 100 4739 5019 .46 2.176 2.28 2.239 2.312 1.384 80 428 2.191 .97 110 3030 18210 43 54 221 232 0 2404 51 2353 1.577 2579 2528 .634 1.652 .657 .725
13 995 983 77 70 918 913 987 937 79 72 910 867 0 0 494 403 13 14 100 100 100 100 1831 1777 1.005 .995 .953 1.055 1.028 1.294 120 609 .946 .97 130 3200 18200 41 54 237 250 0 712 51 662 .721 679 628 1.388 .69 -.473 -.535
14 4156 24759 79 73 4077 24686 3910 18145 82 75 3831 18072 0 0 2328 17655 15 16 100 100 100 100 28763 21903 .165 6.055 4.717 5.602 6.253 1.493 120 570 6.849 .96 120 3370 18200 42 54 255 267 0 17941 53 17888 4.388 13149 13096 .228 3.418 2.133 1.773
15 910 1270 82 72 828 1198 860 1337 83 75 778 1265 0 0 607 667 16 18 100 100 100 100 2026 2043 .691 1.447 1.626 1.57 1.577 1.362 120 591 1.332 .95 130 3570 18220 43 56 274 287 0 920 52 868 1.048 969 917 .954 1.178 .068 .237
16 641 821 79 70 562 751 645 841 81 73 566 771 0 0 294 372 15 21 100 100 100 98 1313 1337 .748 1.336 1.362 1.309 1.385 1.677 120 602 1.336 .96 130 3730 18190 40 53 290 303 0 595 51 544 .968 609 559 1.033 .987 -.046 -.019
17 699 951 83 70 616 881 734 991 85 74 651 921 0 0 316 338 17 23 100 100 100 100 1497 1572 .699 1.43 1.415 1.601 1.404 1.641 80 415 1.364 .92 100 3890 18200 43 53 308 318 0 689 51 638 1.036 718 667 .965 1.025 .052 .036
18 1706 1436 86 71 1620 1365 1327 1376 88 73 1241 1305 0 0 1093 772 15 15 100 99 100 95 2985 2546 1.187 .843 1.052 .747 .932 2.169 120 654 .786 .95 130 4080 18180 39 52 325 338 0 1041 51 989 .611 997 946 1.638 .762 -.712 -.392
19 1375 1381 86 70 1289 1311 1413 1434 87 72 1327 1364 0 0 437 415 14 13 100 100 100 100 2600 2691 .983 1.017 1.028 .992 1.065 1.605 120 585 1.019 .95 130 4250 18190 40 53 342 355 0 1001 51 950 .737 1039 988 1.357 .745 -.44 -.425
20 675 831 87 72 588 759 625 803 88 74 538 731 0 0 287 328 15 15 100 100 99 100 1347 1269 .775 1.291 1.359 1.321 1.297 1.795 120 601 1.278 .92 130 4410 18190 40 53 358 371 0 602 52 550 .935 582 530 1.069 .985 -.096 -.022

Total number of rows: 9600

Table truncated, full table size 2104 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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