|
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.
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|
|
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) |
|
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 |