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Sample GSM258116 Query DataSets for GSM258116
Status Public on Mar 05, 2008
Title F-Genome: slide15
Sample type RNA
 
Channel 1
Source name Fiber at 20 DPA derived from F-genome
Organism Gossypium longicalyx
Characteristics Fiber at 20 DPA derived from F-genome
Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 20 DPA; Parameter Transgenes = none
Extracted molecule total RNA
Extraction protocol Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F20A_A20A_F20c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran
Label Cy3
Label protocol Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/29/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F20A_A20A_F20c5; Parameter Date performed = 1/2/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran
 
Channel 2
Source name Fiber at 20 DPA derived from A-genome
Organism Gossypium herbaceum
Characteristics Fiber at 20 DPA derived from A-genome
Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 20 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none
Treatment protocol Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Extracted molecule total RNA
Extraction protocol Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F20A_A20A_A20c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA
Label Cy5
Label protocol Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/29/2006; 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
Parameter Date performed = 12/22/2006; Parameter Tube label = F20A_A20A_A20c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = Gal file; Software: type: feature extraction
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 = 1/3/2007; 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
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 = 1/3/2007; 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
Description Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57987.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 Jan 22, 2008
Last update date Mar 04, 2008
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 GPL4808
Series (1)
GSE10228 The evolution of spinable cotton fiber entailed prolonged development and a novel metabolism

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
1 331 275 108 109 223 166 341 285 109 109 233 176 0 0 77 53 18 5 100 100 96 100 389 409 1.343 .744 .755 .76 .746 1.188 32 236 .728 .975 70 1260 1710 167 174 122 129 0 238 94 143 .643 246 152 1.555 .653 -.636 -.615
2 116 121 107 108 9 13 116 122 107 108 9 14 0 0 5 5 4 2 81 100 53 93 22 23 .692 1.444 1.556 1.471 1.438 1.944 32 172 1.021 .479 60 1420 1710 168 174 139 145 0 105 93 11 1.248 105 12 .801 1.344 .32 .427
3 473 408 107 108 366 300 499 439 107 108 392 331 0 0 108 95 3 3 100 100 100 100 666 723 1.22 .82 .844 .801 .805 1.166 32 172 .824 .986 60 1550 1710 168 174 152 158 0 353 93 259 .708 379 286 1.412 .73 -.497 -.455
4 221 193 107 108 114 85 222 194 107 108 115 86 0 0 27 20 2 3 100 100 100 100 199 201 1.341 .746 .748 .75 .753 1.147 32 212 .732 .965 70 1710 1710 167 174 167 174 0 167 93 73 .644 168 74 1.552 .646 -.634 -.63
5 109 110 107 108 2 2 108 109 107 108 1 1 0 0 4 4 3 3 32 20 20 7 4 2 1 1 1 .678 .604 2.214 80 418 1.368 .125 100 1850 1700 165 175 180 190 -50 95 93 2 .864 94 1 1.157 .864 -.211 -.211
6 134 137 106 108 28 29 135 143 107 108 29 35 0 0 11 18 3 2 100 86 100 82 57 64 .966 1.036 1.207 .793 1.047 2.137 52 276 1.197 .847 80 2000 1710 167 175 196 204 0 118 93 25 .895 124 30 1.117 1.043 -.16 .061
7 189 135 107 108 82 27 201 137 107 108 94 29 0 0 28 11 4 2 100 100 100 100 109 123 3.037 .329 .309 .319 .317 1.337 32 170 .323 .92 60 2140 1710 168 174 211 217 0 117 93 23 .285 118 25 3.514 .267 -1.813 -1.907
8 112 114 107 109 5 5 112 113 108 109 5 4 0 0 4 4 4 2 53 68 18 43 10 9 1 1 .8 .968 1 2.347 32 171 .87 .211 60 2290 1710 168 174 226 232 0 99 94 4 .864 98 3 1.157 .691 -.211 -.533
9 116 117 113 113 3 4 116 116 114 114 3 3 0 0 4 4 12 12 1 1 0 0 7 6 .75 1.333 1 1.027 1 2.195 80 446 1.021 .528 100 2440 1700 165 175 239 249 -50 101 98 3 1.152 100 3 .868 .864 .204 -.211
10 176 169 114 115 62 54 182 174 114 115 68 59 0 0 20 17 2 2 100 100 100 100 116 127 1.148 .871 .868 .876 .9 1.166 32 224 .864 .953 70 2590 1700 166 173 255 262 0 146 99 47 .753 150 51 1.329 .75 -.41 -.415
11 125 125 113 116 12 9 122 125 113 116 9 9 0 0 7 3 2 2 100 100 100 100 21 18 1.333 .75 1 .869 .805 1.807 12 68 .712 .474 40 2730 1710 169 173 271 275 0 108 100 8 .648 108 8 1.543 .864 -.626 -.211
12 304 5274 112 115 192 5159 119 180 112 115 7 65 0 0 300 8169 2 3 69 100 55 100 5351 72 .037 26.87 9.286 16.564 22.667 2.128 120 608 27.276 .992 120 2880 1700 164 176 282 294 0 4558 99 4458 23.22 156 56 .043 8.024 4.537 3.004
13 118 178 111 114 7 64 117 182 111 114 6 68 0 0 5 17 2 2 84 100 62 100 71 74 .109 9.143 11.333 11.129 10.063 2.157 32 200 9.314 .51 70 3020 1710 167 174 298 305 0 154 99 55 7.901 157 59 .127 9.794 2.982 3.292
14 160 232 111 113 49 119 164 237 111 113 53 124 0 0 15 22 2 2 100 100 100 100 168 177 .412 2.429 2.34 2.516 2.391 1.299 32 176 2.378 .911 60 3170 1700 167 173 314 320 0 200 98 103 2.099 205 107 .476 2.022 1.07 1.016
15 147 171 110 113 37 58 147 177 111 113 37 64 0 0 12 18 5 2 100 100 93 100 95 101 .638 1.568 1.73 1.6 1.567 1.39 32 228 1.551 .813 70 3310 1700 166 173 327 334 0 148 98 50 1.355 153 55 .738 1.495 .438 .58
16 119 141 110 112 9 29 119 142 110 112 9 30 0 0 4 7 2 2 96 100 96 100 38 39 .31 3.222 3.333 3.384 3.267 1.685 32 216 3.475 .565 70 3470 1700 166 173 343 350 0 122 97 25 2.785 123 26 .359 2.881 1.477 1.526
17 118 127 114 116 4 11 117 124 114 116 3 8 0 0 6 12 4 4 42 63 18 48 15 11 .364 2.75 2.667 2.018 2.042 2.572 80 457 2.143 .463 100 3610 1690 164 174 356 366 -50 110 100 10 2.376 107 7 .421 2.304 1.249 1.204
18 250 270 116 117 134 153 255 285 116 118 139 168 0 0 40 45 2 2 100 100 100 100 287 307 .876 1.142 1.209 1.131 1.147 1.167 32 170 1.132 .976 60 3760 1690 166 172 373 379 0 233 101 132 .987 246 145 1.013 1.044 -.019 .063
19 176 183 115 116 61 67 171 181 115 116 56 65 0 0 21 24 2 2 100 100 100 100 128 121 .91 1.098 1.161 1.109 1.154 1.317 32 232 1.08 .885 70 3900 1690 165 172 386 393 0 158 100 58 .949 156 56 1.054 1.003 -.075 .004
20 711 365 116 116 595 249 760 386 116 116 644 270 0 0 231 97 2 2 100 100 100 100 844 914 2.39 .418 .419 .43 .418 1.235 32 236 .408 .984 70 4050 1690 165 172 401 408 0 315 100 215 .362 334 233 2.765 .362 -1.467 -1.465

Total number of rows: 24288

Table truncated, full table size 4866 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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