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Sample GSM29469 Query DataSets for GSM29469
Status Public on Aug 24, 2005
Title DATA:ipe-214; ch1: Pool1: cy3; ch2: Root: cy5
Sample type RNA
 
Channel 1
Source name Pool1: cy3
Organism Saccharum officinarum
Extracted molecule total RNA
 
Channel 2
Source name Root: cy5
Organism Saccharum officinarum
Extracted molecule total RNA
 
 
Description Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference. *low quality
Channel_2: Variety: SP80-3280 Single eyed seed setts from 12 months old field grown plants were treated with the fungicide Benlate (Benomyl) and the insecticide Decis (Deltamethrin)and placed on top of wet paper towels to germinate under dark and moist conditions. Temperature was kept constant at 25oC. After 10 days, adventitious roots were collected and frozen in liquid nitrogen and stored at -80oC.
Hybridization: micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
Channel_1 RNA extraction: Trizol; Channel_2 RNA extraction: Guanidine-HCl
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.
 
Submission date Aug 24, 2004
Last update date May 28, 2005
Contact name Renato Vicentini
E-mail(s) shinapes@unicamp.br
Phone 55-19-35211101
Fax 55-19-37881089
URL http://sysbiol.cbmeg.unicamp.br
Organization name Universidade Estadual de Campinas - UNICAMP
Department Centro de Biologia Molecular e Engenharia Genetica - CBMEG
Lab Systems Biology Laboratory
Street address Cidade Universitaria "Zeferino Vaz"
City Campinas
State/province SP
ZIP/Postal code 13083-875
Country Brazil
 
Platform ID GPL1375
Series (1)
GSE1702 The SUCAST catalogue

Data table header descriptions
ID_REF ID_REF
X X coordinate on array; Type: Int; Scale: Linear
Y Y coordinate on array; Type: Int; Scale: Linear
dia Spot diameter; Type: Int; Scale: Linear
FCh1Median Foreground channel 1 median. Channel 1 is the numerator in ratios.; Type: Float; Scale: Linear
FCh1Mean Foreground channel 1 mean; Type: Float; Scale: Linear
FCh1SD Foreground channel 1 standard deviation; Type: Float; Scale: Linear
BCh1Median Background channel 1 median; Type: Float; Scale: Linear
BCh1Mean Background channel 1 mean; Type: Float; Scale: Linear
BCh1SD Background channel 1 standard deviation; Type: Float; Scale: Linear
percCh1SD1 Percentage of channel 1 pixels within 1 standard deviation; Type: Float; Scale: Linear
percCh1SD2 Percentage of channel 1 pixels within 1 standard deviation = Percentage of channel 1 pixels within 1 standard deviation; Type: Float; Scale: Linear
percCh1Sat Percentage of channel 1 pixels saturated; Type: Float; Scale: Linear
FCh2Median Foreground channel 2 median. Channel 2 is the denominator in ratios.; Type: Float; Scale: Linear
FCh2Mean Foreground channel 2 mean; Type: Float; Scale: Linear
FCh2SD Foreground channel 2 standard deviation; Type: Float; Scale: Linear
BCh2Median Background channel 2 median; Type: Float; Scale: Linear
BCh2Mean Background channel 2 mean; Type: Float; Scale: Linear
BCh2SD Background channel 2 standard deviation; Type: Float; Scale: Linear
percCh2SD1 Percentage of channel 2 pixels within 1 standard deviation; Type: Int; Scale: Linear
percCh2SD2 Percentage of channel 2 pixels within 1 standard deviation; Type: Int; Scale: Linear
percCh2Sat Percentage of channel 2 pixels saturated; Type: Int; Scale: Linear
ratiosSD Standard deviation of ratios; Type: Float; Scale: Linear
VALUE log ratio (log2 of PRE_VALUE)
rgnR2 Regression R-squared; Type: Float; Scale: Linear
FPixels Foreground pixels; Type: Int; Scale: Linear
BPixels Background pixels; Type: Int; Scale: Linear
flags Spot flags; Type: Int; Scale: Other
Mvalue M value; Type: Float; Scale: Linear
CV Confidence value; Type: Float; Scale: Linear
PRE_VALUE Regression ratio. The ratio is channel 1 / channel 2, regardless of how they were labeled; Type: Float; Scale: Linear

Data table
ID_REF X Y dia FCh1Median FCh1Mean FCh1SD BCh1Median BCh1Mean BCh1SD percCh1SD1 percCh1SD2 percCh1Sat FCh2Median FCh2Mean FCh2SD BCh2Median BCh2Mean BCh2SD percCh2SD1 percCh2SD2 percCh2Sat ratiosSD VALUE rgnR2 FPixels BPixels flags Mvalue CV PRE_VALUE
F:ipe-25-1-1-1 255 49865 25600 0 155.182 48.475 17.277 0 0 0 0 0 0 671.555 222.095 5.028 0 0 0 0 1 0 -2.2722973 0 0 0 0 0 0 0.207
F:ipe-25-1-1-2 525 49845 25600 0 119.058 31.779 17.96 0 0 0 0 0 0 493.333 134.155 5.401 0 0 0 0 0 0 -2.2722973 0 0 0 0 0 0 0.207
F:ipe-25-1-1-3 775 49855 25600 0 40.756 9.331 18.411 0 0 0 0 0 0 113.804 38.741 5.27 0 0 0 0 0 0 -2.2792843 0 0 0 0 0 0 0.206
F:ipe-25-1-1-4 1035 49855 25600 0 28.218 3.538 19.023 0 0 0 0 0 0 47.338 14.424 5.13 0 0 0 0 0 0 -2.1976003 0 0 0 0 0 0 0.218
F:ipe-25-1-1-5 1305 49855 25600 0 21.936 1.277 19.197 0 0 0 0 0 0 21.322 4.791 5.011 0 0 0 0 0 0 -2.5734673 0 0 0 0 0 0 0.168
F:ipe-25-1-1-6 1605 49845 25600 0 21.161 1.085 19.308 0 0 0 0 0 0 13.225 1.835 5.082 0 0 0 0 0 0 -2.1328943 0 0 0 0 0 0 0.228
F:ipe-25-1-1-7 1875 49845 25600 0 19.773 1.18 19.351 0 0 0 0 0 0 6.781 0.726 4.92 0 0 0 0 0 0 -2.1392363 0 0 0 0 0 0 0.227
F:ipe-25-1-1-8 2155 49845 25600 0 20.018 1.022 19.387 0 0 0 0 0 0 6.247 0.882 4.863 0 0 0 0 0 0 -1.1328943 0 0 0 0 0 0 0.456
F:ipe-25-1-1-9 2435 49845 25600 0 19.507 0.946 19.354 0 0 0 0 0 0 4.996 0.499 4.892 0 0 0 0 0 0 0.5616933 0 0 0 0 0 0 1.476
F:ipe-25-1-1-10 2725 49845 25600 0 19.355 1.031 19.299 0 0 0 0 0 0 4.913 0.526 4.921 0 0 0 0 0 0 0 0 0 0 0 0
F:ipe-25-1-1-11 2975 49865 25600 0 49.909 10.305 19.284 0 0 0 0 0 0 59.768 16.175 5.064 0 0 0 0 0 0 -0.8365013 0 0 0 0 0 0 0.56
F:ipe-25-1-1-12 3265 49855 25600 0 28.057 2.58 19.179 0 0 0 0 0 0 119.916 23.449 5.352 0 0 0 0 0 0 -3.6989983 0 0 0 0 0 0 0.077
F:ipe-25-1-2-1 3545 49865 25600 0 20.337 1.073 18.924 0 0 0 0 0 0 7.819 0.927 5.29 0 0 0 0 0 0 -0.8390803 0 0 0 0 0 0 0.559
F:ipe-25-1-2-2 3825 49845 25600 0 19.946 1.018 18.855 0 0 0 0 0 0 17.817 3.106 5.031 0 0 0 0 0 0 -3.5563933 0 0 0 0 0 0 0.085
F:ipe-25-1-2-3 4125 49845 25600 0 18.679 0.831 18.969 0 0 0 0 0 0 5.529 0.649 4.968 0 0 0 0 0 0 0 0 0 0 0 0 0
F:ipe-25-1-2-4 4395 49855 25600 0 21.41 0.992 18.641 0 0 0 0 0 0 6.305 0.613 4.927 0 0 0 0 0 0 1.0071963 0 0 0 0 0 0 2.01
F:ipe-25-1-2-5 4675 49855 25600 0 18.863 0.994 18.408 0 0 0 0 0 0 16.852 4.044 4.738 0 0 0 0 0 0 -4.7178573 0 0 0 0 0 0 0.038
F:ipe-25-1-2-6 4955 49855 25600 0 103.015 29.185 18.37 0 0 0 0 0 0 49.764 13.879 4.574 0 0 0 0 0 0 0.9053513 0 0 0 0 0 0 1.873
F:ipe-25-1-2-7 5255 49855 25600 0 28.122 3.122 18.261 0 0 0 0 0 0 464.883 143.811 4.713 0 0 0 0 0 0 -5.5734673 0 0 0 0 0 0 0.021
F:ipe-25-1-2-8 5565 49845 25600 0 18.186 0.757 18.176 0 0 0 0 0 0 4.818 0.605 4.673 0 0 0 0 0 0 -3.8365013 0 0 0 0 0 0 0.07

Total number of rows: 3840

Table truncated, full table size 469 Kbytes.




Supplementary data files not provided
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