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Sample GSM29465 Query DataSets for GSM29465
Status Public on Aug 24, 2005
Title DATA:ipe-210; ch1: Flower: cy3; ch2: Pool1: cy5
Sample type RNA
 
Channel 1
Source name Flower: 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: Variety: SP87-342 Sampling date: 05/09/2003 Planting date: 08/26/2002 as single stools from potted plants Tissue: Inflorescence Tissue description: Several immature inflorescences with lengths varying between 5 and 30 cm were sampled and stored at -80oC. Small pieces of the inflorescences containing all its different tissue types were pooled from freezer for RNA extraction.
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-25-1-1-1 645 49655 25600 0 515.54 165.838 12.851 0 0 0 0 0 0 645.234 218.619 3.507 0 0 0 0 0 0 -0.3529163 0 0 0 0 0 0 0.783
F:ipe-25-1-1-2 895 49655 25600 0 566.063 131.451 13.293 0 0 0 0 0 0 799.827 190.863 3.669 0 0 0 0 0 0 -0.5269923 0 0 0 0 0 0 0.694
F:ipe-25-1-1-3 1165 49655 25600 0 209.533 50.003 13.404 0 0 0 0 0 0 236.509 61.235 3.615 0 0 0 0 0 0 -0.2481083 0 0 0 0 0 0 0.842
F:ipe-25-1-1-4 1445 49655 25600 0 108.628 25.806 13.623 0 0 0 0 0 0 120.359 31.594 3.609 0 0 0 0 0 0 -0.2968993 0 0 0 0 0 0 0.814
F:ipe-25-1-1-5 1705 49655 25600 0 41.031 8.744 13.944 0 0 0 0 0 0 36.989 11.059 3.71 0 0 0 0 0 0 -0.2968993 0 0 0 0 0 0 0.814
F:ipe-25-1-1-6 1985 49655 25600 0 25.93 2.827 14.241 0 0 0 0 0 0 18.282 3.319 3.868 0 0 0 0 0 0 -0.3022263 0 0 0 0 0 0 0.811
F:ipe-25-1-1-7 2255 49665 25600 0 18.753 1.376 14.329 0 0 0 0 0 0 9.676 1.682 3.723 0 0 0 0 0 0 -0.4285663 0 0 0 0 0 0 0.743
F:ipe-25-1-1-8 2525 49645 25600 0 15.713 0.803 14.365 0 0 0 0 0 0 5.645 0.601 3.731 0 0 0 0 0 0 -0.5063533 0 0 0 0 0 0 0.704
F:ipe-25-1-1-9 2845 49645 25600 0 14.633 0.745 14.371 0 0 0 0 0 0 4.059 0.769 3.703 0 0 0 0 0 0 -0.4383073 0 0 0 0 0 0 0.738
F:ipe-25-1-1-10 3135 49645 25600 0 14.343 0.712 14.308 0 0 0 0 0 0 3.959 0.452 3.636 0 0 0 0 0 0 -3.2243173 0 0 0 0 0 0 0.107
F:ipe-25-1-1-11 3375 49655 25600 0 71.651 16.54 14.48 0 0 0 0 0 0 189.564 51.295 3.664 0 0 0 0 0 0 -1.6989983 0 0 0 0 0 0 0.308
F:ipe-25-1-1-12 3665 49655 25600 0 167.278 32.365 14.405 0 0 0 0 0 0 85.945 17.455 3.6 0 0 0 0 0 0 0.8921973 0 0 0 0 0 0 1.856
F:ipe-25-1-2-1 3955 49655 25600 0 19.11 1.515 14.355 0 0 0 0 0 0 20.222 3.949 3.6 0 0 0 0 0 0 -1.8059133 0 0 0 0 0 0 0.286
F:ipe-25-1-2-2 4235 49655 25600 0 34.609 4.516 14.418 0 0 0 0 0 0 12.894 1.972 3.631 0 0 0 0 0 0 1.1243283 0 0 0 0 0 0 2.18
F:ipe-25-1-2-3 4545 49645 25600 0 15.212 0.809 14.428 0 0 0 0 0 0 4.644 0.521 3.627 0 0 0 0 0 0 -0.3751973 0 0 0 0 0 0 0.771
F:ipe-25-1-2-4 4815 49655 25600 0 17.171 2.685 14.386 0 0 0 0 0 0 31.88 5.129 3.573 0 0 0 0 0 0 -3.3510743 0 0 0 0 0 0 0.098
F:ipe-25-1-2-5 5105 49655 25600 0 33.602 5.241 14.438 0 0 0 0 0 0 6.061 0.889 3.592 0 0 0 0 0 0 2.9560573 0 0 0 0 0 0 7.76
F:ipe-25-1-2-6 5405 49655 25600 0 55.656 7.109 14.658 0 0 0 0 0 0 474.295 78.692 3.643 0 0 0 0 0 0 -3.5228413 0 0 0 0 0 0 0.087
F:ipe-25-1-2-7 5685 49655 25600 0 460.525 129.095 15.045 0 0 0 0 0 0 53.937 15.094 3.665 0 0 0 0 0 0 3.1474703 0 0 0 0 0 0 8.861
F:ipe-25-1-2-8 5985 49645 25600 0 15.147 0.81 15.474 0 0 0 0 0 0 3.667 0.359 3.77 0 0 0 0 0 0 0 0 0 0 0 0 0

Total number of rows: 3840

Table truncated, full table size 466 Kbytes.




Supplementary data files not provided
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