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Sample GSM1115464 Query DataSets for GSM1115464
Status Public on Apr 05, 2013
Title SRP54 IP YPAD mid-log phase 5mM MgCl2/cyclohexamide (9)
Sample type RNA
 
Channel 1
Source name total rna extract
Organism Saccharomyces cerevisiae
Characteristics reference: total rna
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name affinity purified RNA
Organism Saccharomyces cerevisiae
Characteristics cyclohexamide treatment: +
genotype: wt
tap-tag: SRP54
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 80, 6040; Software: type: feature extraction; Performer: Daniel,,Hogan
Description Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77583.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 Apr 04, 2013
Last update date Apr 05, 2013
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL16964
Series (2)
GSE45794 RNA coimmunoprecipitations
GSE45798 Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes.

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
1 169 104 55 56 114 48 171 103 55 57 116 47 0 0 21 15 6 8 100 100 100 100 162 163 2.375 .421 .405 .406 .405 1.464 52 400 .399 .86 90 2610 14550 846 855 248 257 0 158 85 73 .638 156 71 1.567 .614 -.648 -.704
2 629 270 54 56 575 214 635 271 57 57 581 215 0 0 73 32 26 11 100 100 100 100 789 796 2.687 .372 .37 .372 .377 1.146 52 380 .373 .98 90 2780 14550 846 855 265 274 0 409 85 324 .564 411 326 1.773 .561 -.826 -.835
3 380 272 54 56 326 216 386 271 62 60 332 215 0 0 52 36 43 24 100 100 100 100 542 547 1.509 .663 .648 .664 .669 1.226 52 355 .656 .96 90 2940 14550 846 855 281 290 0 412 85 327 1.004 411 326 .996 .981 .006 -.027
4 1368 3054 54 57 1314 2997 1465 3204 59 61 1411 3147 0 0 312 556 32 24 100 100 100 100 4311 4558 .438 2.281 2.23 2.323 2.233 1.122 80 480 2.229 .99 110 3110 14560 846 857 297 308 0 4628 86 4542 3.456 4855 4769 .289 3.38 1.789 1.757
5 597 267 55 57 542 210 630 270 55 58 575 213 0 0 139 47 11 17 100 100 100 100 752 788 2.581 .387 .37 .392 .388 1.218 80 414 .369 .97 100 3280 14550 846 856 315 325 0 405 86 318 .587 409 323 1.703 .561 -.768 -.833
6 966 390 55 57 911 333 982 400 56 58 927 343 0 0 173 61 15 10 100 100 100 100 1244 1270 2.736 .366 .37 .366 .368 1.159 80 427 .353 .98 100 3440 14550 846 856 331 341 0 591 86 505 .554 606 520 1.805 .561 -.852 -.835
7 631 505 55 58 576 447 664 516 56 59 609 458 0 0 118 84 12 10 100 100 100 100 1023 1067 1.289 .776 .752 .782 .773 1.156 80 462 .76 .98 100 3620 14540 845 855 349 359 0 765 88 677 1.176 782 694 .85 1.14 .234 .189
8 505 277 55 57 450 220 519 279 56 58 464 222 0 0 90 43 12 8 100 100 100 100 670 686 2.045 .489 .478 .489 .484 1.19 80 440 .479 .98 100 3790 14540 845 855 366 376 0 420 86 333 .741 423 336 1.35 .725 -.433 -.464
9 340 191 55 58 285 133 353 195 55 58 298 137 0 0 58 33 5 8 100 100 100 100 418 435 2.143 .467 .46 .462 .468 1.219 80 440 .459 .96 100 3960 14540 845 855 383 393 0 289 88 202 .707 295 208 1.414 .697 -.5 -.521
10 2930 1272 54 57 2876 1215 2965 1323 55 58 2911 1266 0 0 524 207 8 8 100 100 100 100 4091 4177 2.367 .422 .435 .423 .421 1.089 80 496 .417 .99 110 4130 14540 844 855 399 410 0 1928 86 1841 .64 2005 1918 1.562 .659 -.643 -.602
11 495 206 55 57 440 149 513 204 55 59 458 147 0 0 86 32 9 10 100 100 100 100 589 605 2.953 .339 .321 .339 .328 1.211 80 440 .325 .97 100 4300 14540 845 855 417 427 0 312 86 226 .513 309 223 1.949 .486 -.963 -1.04
12 547 176 56 57 491 119 574 178 57 58 518 121 0 0 99 28 14 8 100 100 100 100 610 639 4.126 .242 .234 .24 .239 1.223 80 437 .235 .96 100 4470 14540 845 855 434 444 0 267 86 180 .367 270 183 2.723 .354 -1.445 -1.498
13 4324 1530 56 57 4268 1473 4680 1620 57 59 4624 1563 0 0 863 264 32 12 100 100 100 100 5741 6187 2.897 .345 .338 .347 .342 1.09 80 439 .337 .99 100 4630 14550 846 856 450 460 0 2319 86 2232 .523 2455 2369 1.912 .512 -.935 -.965
14 488 226 57 59 431 167 508 231 58 60 451 172 0 0 90 43 32 12 100 100 100 100 598 623 2.581 .387 .381 .381 .393 1.221 80 438 .382 .97 100 4810 14550 846 856 468 478 0 342 89 253 .587 350 261 1.703 .578 -.768 -.791
15 137 121 56 59 81 62 142 123 56 60 86 64 0 0 28 24 5 8 96 100 96 96 143 150 1.306 .765 .744 .78 .776 1.61 80 426 .76 .91 100 4970 14550 846 856 484 494 0 183 89 94 1.16 186 97 .862 1.128 .214 .173
16 637 228 56 59 581 169 668 233 57 59 612 174 0 0 124 37 5 8 100 100 100 100 750 786 3.438 .291 .284 .291 .293 1.183 80 440 .284 .97 100 5140 14550 846 856 501 511 0 346 89 256 .441 353 264 2.269 .431 -1.182 -1.215
17 1286 695 57 59 1229 636 1376 718 57 59 1319 659 0 0 254 117 6 9 100 100 100 100 1865 1978 1.932 .517 .5 .521 .517 1.144 80 436 .506 .99 100 5310 14550 846 856 518 528 0 1053 89 964 .784 1088 999 1.275 .757 -.351 -.401
18 562 220 55 59 507 161 593 225 56 59 538 166 0 0 107 37 7 8 100 100 100 100 668 704 3.149 .318 .309 .318 .314 1.212 80 438 .31 .97 100 5470 14550 846 856 534 544 0 333 89 244 .481 341 252 2.078 .468 -1.055 -1.097
19 98 86 56 59 42 27 97 84 56 59 41 25 0 0 13 13 6 9 100 91 100 72 69 66 1.556 .643 .61 .606 .655 1.807 80 452 .71 .73 100 5650 14550 846 856 552 562 0 130 89 41 .974 127 38 1.027 .924 -.038 -.114
20 779 302 56 58 723 244 850 310 56 59 794 252 0 0 173 67 5 8 100 100 100 100 967 1046 2.963 .337 .317 .331 .336 1.213 80 440 .337 .98 100 5820 14550 846 856 569 579 0 458 88 370 .511 470 382 1.955 .481 -.967 -1.056

Total number of rows: 19968

Table truncated, full table size 4262 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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