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Sample GSM29466 Query DataSets for GSM29466
Status Public on Aug 24, 2005
Title DATA:ipe-211; ch1: Stem4: cy3; ch2: Pool1: cy5
Sample type RNA
 
Channel 1
Source name Stem4: cy3
Organism Saccharum officinarum
Extracted molecule total RNA
 
Channel 2
Source name Pool1: cy5
Organism Saccharum officinarum
Extracted molecule total RNA
 
 
Description Origin: Sugarcane
Channel_1: The fourth internode , visible after leaf removal and counted from top of the plant was collected from a single 12 month old field grown plant of the commercial variety SP80-3280. The nodal region was discarded and the tissue was sectioned in small pieces that were frozen in liquid nitrogen and stored at -80oC
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference. *low quality
Hybridization: micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
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-25-1-1-1 615 50125 25600 0 92.178 28.906 15.92 0 0 0 0 0 0 424.207 151.164 6.527 0 0 0 0 0 0 -2.4500843 0 0 0 0 0 0 0.183
F:ipe-25-1-1-2 865 50135 25600 0 84.387 23.625 16.129 0 0 0 0 0 0 295.188 103.683 6.888 0 0 0 0 0 0 -2.0770413 0 0 0 0 0 0 0.237
F:ipe-25-1-1-3 1135 50135 25600 0 32.473 4.133 16.342 0 0 0 0 0 0 71.093 15.033 7.268 0 0 0 0 0 0 -1.9827913 0 0 0 0 0 0 0.253
F:ipe-25-1-1-4 1415 50125 25600 0 23.846 2.027 16.378 0 0 0 0 0 0 35.825 7.502 7.015 0 0 0 0 0 0 -1.9489763 0 0 0 0 0 0 0.259
F:ipe-25-1-1-5 1685 50125 25600 0 19.099 1.025 16.345 0 0 0 0 0 0 17.205 3.189 6.532 0 0 0 0 0 0 -1.9545573 0 0 0 0 0 0 0.258
F:ipe-25-1-1-6 1945 50125 25600 0 18.273 1.112 16.295 0 0 0 0 0 0 12.15 2.023 6.466 0 0 0 0 0 0 -1.5228413 0 0 0 0 0 0 0.348
F:ipe-25-1-1-7 2215 50125 25600 0 17.349 0.907 16.387 0 0 0 0 0 0 8.622 0.92 6.747 0 0 0 0 0 0 -0.9629693 0 0 0 0 0 0 0.513
F:ipe-25-1-1-8 2505 50115 25600 0 16.916 1.279 16.273 0 0 0 0 0 0 7.793 2.385 6.975 0 0 0 0 0 0 -0.3473993 0 0 0 0 0 0 0.786
F:ipe-25-1-1-9 2795 50115 25600 0 16.588 0.879 15.596 0 0 0 0 0 0 7.046 0.751 6.973 0 0 0 0 0 0 3.7661713 0 0 0 0 0 0 13.606
F:ipe-25-1-1-10 3085 50115 25600 0 16.075 0.839 15.423 0 0 0 0 0 0 7.035 0.704 7.068 0 0 0 0 0 0 0 0 0 0 0 0
F:ipe-25-1-1-11 3335 50125 25600 0 27.429 4.001 15.237 0 0 0 0 0 0 145.453 38.679 6.968 0 0 0 0 0 0 -3.5063533 0 0 0 0 0 0 0.088
F:ipe-25-1-1-12 3615 50125 25600 0 44.26 6.11 15.053 0 0 0 0 0 0 55.786 9.032 6.858 0 0 0 0 0 0 -0.7441973 0 0 0 0 0 0 0.597
F:ipe-25-1-2-1 3885 50135 25600 0 16.422 0.954 14.83 0 0 0 0 0 0 14.587 2.299 6.813 0 0 0 0 0 0 -2.2863043 0 0 0 0 0 0 0.205
F:ipe-25-1-2-2 4175 50135 25600 0 18.25 1.254 14.751 0 0 0 0 0 0 11.755 1.417 6.707 0 0 0 0 0 0 -0.5290733 0 0 0 0 0 0 0.693
F:ipe-25-1-2-3 4495 50115 25600 0 15.049 0.806 14.624 0 0 0 0 0 0 7.232 0.772 6.656 0 0 0 0 0 0 -0.4402633 0 0 0 0 0 0 0.737
F:ipe-25-1-2-4 4765 50135 25600 0 15.186 0.918 14.337 0 0 0 0 0 0 18.822 3.179 6.482 0 0 0 0 0 0 -3.8572603 0 0 0 0 0 0 0.069
F:ipe-25-1-2-5 5035 50125 25600 0 17.138 1.076 14.194 0 0 0 0 0 0 7.956 0.797 6.408 0 0 0 0 0 0 0.9275173 0 0 0 0 0 0 1.902
F:ipe-25-1-2-6 5345 50135 25600 0 23.337 2.93 13.921 0 0 0 0 0 0 393.758 96.521 6.566 0 0 0 0 0 0 -5.3808223 0 0 0 0 0 0 0.024
F:ipe-25-1-2-7 5645 50125 25600 0 122.115 36.212 13.771 0 0 0 0 0 0 52.117 14.982 6.95 0 0 0 0 0 0 1.2624333 0 0 0 0 0 0 2.399
F:ipe-25-1-2-8 5945 50115 25600 0 14.528 0.753 13.87 0 0 0 0 0 0 7.143 0.614 6.986 0 0 0 0 0 0 2.0610853 0 0 0 0 0 0 4.173

Total number of rows: 3840

Table truncated, full table size 468 Kbytes.




Supplementary data files not provided
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