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Sample GSM136813 Query DataSets for GSM136813
Status Public on Sep 22, 2006
Title Microarray Design (slide 67): bud vs. bud'
Sample type RNA
 
Channel 1
Source Name bud with Cy5
Organism(s) Gossypium hirsutum
Characteristics bud with Cy5
Parameter Accession number or name = Maxxa; Parameter Species = Gossypium hirsutum; Parameter Genome = AD1; Parameter Polyploid level = 4x; Parameter Tissue type = buds; Parameter Transgenes = none; Performer: Joshua,,Udall
Treatment protocol Parameter Genome = AD; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse / Bessey Hall / Ames, IA; Performer: Joshua,,Udall
Extracted molecule total RNA
Extraction protocol Parameter Date performed = May-06; Parameter Extraction method reference = Wilkins and Smart, 1996; Parameter Channel 1 reference name = Buds; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = A bulk of buds from 4-5 plants; Parameter Extracted molecule = RNA; Parameter Name = Josh and Lex; Performer: Joshua,,Udall
Label Cy5
Label protocol Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug (buds); Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 5/31/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug; Performer: Joshua,,Udall
Protocol Type = Labeling; Parameter Tube label = 1; Parameter Date performed = 6/5/2006; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 24 ug; Parameter Type of label = Cy5; Parameter Name = Ran; Performer: Joshua,,Udall
 
Channel 2
Source Name bud' with Cy3
Organism(s) Gossypium hirsutum
Characteristics bud' with Cy3
Parameter Accession number or name = Maxxa; Parameter Species = Gossypium hirsutum; Parameter Genome = AD1; Parameter Tissue type = buds; Parameter Polyploid level = 4x; Parameter Transgenes = none; Performer: Joshua,,Udall
Treatment protocol Parameter Genome = AD; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse / Bessey Hall / Ames, IA; Performer: Joshua,,Udall
Extracted molecule total RNA
Extraction protocol Parameter Date performed = May-06; Parameter Extraction method reference = Wilkins and Smart, 1996; Parameter Channel 2 reference name = Buds; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = A bulk of buds from 4-5 plants; Parameter Name = Josh and Lex; Parameter Extracted molecule = RNA; Performer: Joshua,,Udall
Label Cy3
Label protocol Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug (buds); Parameter Date performed = 5/31/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug; Performer: Joshua,,Udall
Protocol Type = Labeling; Parameter Date performed = 6/5/2006; Parameter Tube label = 2; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 24 ug; Parameter Type of label = Cy3; Parameter Name = Ran; Performer: Joshua,,Udall
 
 
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter RatioFormulations = W1/W2 (685 nm/595); Parameter StdDev = Type 1; Parameter BackgroundSubtraction = LocalFeature; Parameter PixelSize = 10; Parameter NormalizationFactors = 1 1; Parameter ImageOrigin = 0, 0; Parameter FeatureType = Circular; Parameter LinesAveraged = 1; Parameter JpegOrigin = 2450, 740; Parameter DateTime = 2006/06/05 12:07:36; Parameter ScanRegion = 0,0,2251,5797; Parameter NormalizationMethod = None; Parameter Wavelengths = 685 nm 595; Parameter Image Origin = 0, 0; Parameter Type = GenePix Results 3; Parameter Datafile type = Gal file; Software: type: feature extraction; Performer: Joshua,,Udall
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 6/7/2006; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite; Performer: Joshua,,Udall
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 6/7/2006; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite; Performer: Joshua,,Udall
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs/2006-07/57911.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 Sep 19, 2006
Contact name Alan R Gingle
E-mail(s) agingle@uga.edu
Organization name University of Georgia
Department Center for Applied Genetics Technologies
Lab Gingle lab
Street address 111 Riverbend Rd.
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
 
Platform ID GPL4305
Series (1)
GSE5875 Cotton spotted oligonucleotide microarrays for gene expression analysis

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 1023 488 257 410 766 78 1090 493 255 409 833 83 0 0 356 39 13 14 100 93 100 90 844 916 9.821 .102 .1 .097 .113 2.044 32 176 .101 .854 60 2620 960 93 99 259 265 0 2773 2329 443 .579 2801 472 1.728 .566 -.789 -.821
2 556 428 252 406 304 22 561 426 253 406 309 20 0 0 123 17 12 14 100 62 100 37 326 329 13.818 .072 .065 .069 .075 2.811 32 236 .048 .135 70 2810 960 92 99 277 284 0 2432 2307 125 .411 2420 114 2.432 .368 -1.282 -1.443
3 3227 715 252 410 2975 305 3410 733 253 412 3158 323 0 0 1058 118 15 15 100 100 100 100 3280 3481 9.754 .103 .102 .1 .106 1.211 32 236 .101 .95 70 2980 970 93 100 294 301 0 4062 2329 1733 .582 4165 1835 1.717 .581 -.78 -.783
4 946 475 249 412 697 63 890 472 249 410 641 60 0 0 402 32 13 15 100 93 100 90 760 701 11.063 .09 .094 .099 .086 1.74 32 176 .083 .748 60 3170 960 93 99 314 320 0 2699 2341 358 .514 2682 341 1.947 .532 -.961 -.911
5 457 416 251 409 206 7 477 414 250 408 226 5 0 0 92 14 12 12 100 31 100 12 213 231 29.429 .034 .022 .051 .054 2.629 32 236 .042 .08 70 3370 950 91 98 333 340 0 2364 2324 40 .193 2352 28 5.18 .126 -2.373 -2.992
6 449 412 257 406 192 6 452 415 263 408 195 9 0 0 88 13 31 16 100 15 93 0 198 204 32 .031 .046 .059 .065 2.409 32 176 .043 .082 60 3560 950 92 98 353 359 0 2341 2307 34 .178 2358 51 5.632 .262 -2.494 -1.931
7 413 433 273 405 140 28 401 419 272 406 128 14 0 0 94 60 14 13 93 53 90 15 168 142 5 .2 .109 .154 .14 2.48 32 176 .332 .454 60 3740 950 92 98 371 377 0 2460 2301 159 1.136 2381 80 .88 .621 .184 -.686
8 392 415 272 404 120 11 397 418 272 403 125 14 0 0 54 14 12 12 96 56 96 18 131 139 10.909 .092 .112 .153 .143 2.194 32 236 .084 .108 70 3930 950 91 98 389 396 0 2358 2295 62 .521 2375 80 1.92 .636 -.941 -.652
9 332 410 277 405 55 5 329 409 278 405 52 4 0 0 19 12 16 13 100 41 91 0 60 56 11 .091 .077 .181 .292 2.575 12 68 .081 .011 40 4120 970 95 99 410 414 0 2329 2301 28 .517 2324 23 1.936 .437 -.953 -1.194
10 1139 496 274 402 865 94 1259 504 273 403 985 102 0 0 487 46 12 13 100 100 100 93 959 1087 9.202 .109 .104 .123 .11 1.611 32 236 .102 .882 70 4300 950 91 98 426 433 0 2818 2284 534 .617 2864 580 1.62 .588 -.696 -.765
11 295 404 277 405 18 -1 295 405 278 405 18 0 0 0 16 13 15 13 57 15 13 0 17 18 null null null .497 .615 3.99 52 340 .183 .009 80 4490 950 91 99 445 453 -50 2295 2301 -6 null 2301 0 null null null null
12 3310 701 282 407 3028 294 3706 723 282 407 3424 316 0 0 910 76 16 14 100 100 100 100 3322 3740 10.299 .097 .092 .099 .096 1.185 32 236 .094 .96 70 4660 950 91 98 462 469 0 3983 2312 1670 .552 4108 1795 1.813 .524 -.858 -.931
13 290 403 277 406 13 -3 287 403 278 405 10 -3 0 0 13 12 13 13 38 11 15 1 10 7 null null null .612 .8 4.18 52 340 -.313 .003 80 4860 950 91 99 482 490 -50 2290 2307 -17 null 2290 -17 null null null null
14 2536 659 273 403 2263 256 2873 671 274 402 2600 268 0 0 1225 139 12 13 100 100 100 96 2519 2868 8.84 .113 .103 .115 .115 1.367 32 236 .111 .961 70 5050 950 91 98 501 508 0 3744 2290 1455 .643 3812 1523 1.556 .586 -.638 -.772
15 1035 484 272 402 763 82 1171 483 273 400 899 81 0 0 337 41 12 13 100 96 100 90 845 980 9.305 .107 .09 .107 .113 1.39 32 236 .109 .846 70 5240 950 91 98 520 527 0 2750 2284 466 .611 2744 460 1.638 .512 -.712 -.966
16 343 407 272 399 71 8 346 408 272 399 74 9 0 0 35 14 12 12 94 34 88 7 79 83 8.875 .113 .122 .19 .182 2.72 52 340 .114 .088 80 5420 950 91 99 538 546 0 2312 2267 45 .64 2318 51 1.562 .691 -.643 -.533
17 1023 523 271 401 752 122 1018 515 277 401 747 114 0 0 295 60 43 14 100 100 100 100 874 861 6.164 .162 .153 .155 .163 1.256 32 176 .169 .936 60 5610 950 92 98 558 564 0 2972 2278 693 .922 2926 648 1.085 .867 -.118 -.206
18 2715 675 269 398 2446 277 3068 682 268 399 2799 284 0 0 1141 132 12 12 100 100 100 100 2723 3083 8.83 .113 .101 .111 .111 1.385 32 176 .111 .954 60 5800 950 92 98 577 583 0 3835 2261 1574 .643 3875 1614 1.554 .576 -.636 -.795
19 1624 529 268 401 1356 128 1663 536 267 401 1395 135 0 0 402 45 13 13 100 100 100 96 1484 1530 10.594 .094 .097 .092 .094 1.255 32 236 .095 .905 70 6010 970 93 100 597 604 0 3006 2278 727 .536 3045 767 1.865 .55 -.899 -.863
20 5778 1013 270 402 5508 611 6735 1113 270 402 6465 711 0 0 2336 245 13 14 100 100 100 100 6119 7176 9.015 .111 .11 .114 .111 1.155 32 236 .109 .986 70 6170 950 91 98 613 620 0 5756 2284 3472 .63 6324 4040 1.587 .625 -.666 -.678

Total number of rows: 26880

Table truncated, full table size 5894 Kbytes.




Supplementary file Size Download File type/resource
GSM136813.gpr.gz 2.2 Mb (ftp)(http) GPR
Raw data provided as supplementary file
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