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Sample GSM123809 Query DataSets for GSM123809
Status Public on Jul 31, 2006
Title 15dpi rep A Pathogen (Cy5) vs. Mycorrhiza (Cy3) (12780946)
Sample type RNA
 
Channel 1
Source name Pinus sylvestris root tissues rep A Pathogen (Cy5)
Organism Pinus sylvestris
Characteristics Pinus sylvestris roots challenged for 15 days with: Pathogen (Heterobasidion annosum)
Treatment protocol Pinus sylvestris seedlings (14 days post-germination) were inoculated with homogenized mycelium of Heterobasidion annosum and harvested at 15dpi. Total RNA was extracted and used for cDNA synthesis with SMART PCR cDNA synthesis kit (Clontech, USA).
Extracted molecule total RNA
Label Cy5
Label protocol The cDNA generated from the roots was labelled using a Klenow method following the protocol from North Carolina State University (van Zyl, U.S. Provisional Patent Application Nos. 60/372,872 and 60/390,142).
 
Channel 2
Source name rep A Mycorrhiza (Cy3)
Organism Pinus sylvestris
Characteristics Pinus sylvestris challenged for 15 days with: Mycorrhiza (Laccaria bicolor)
Treatment protocol Pinus sylvestris seedlings (14 days post-germination) were inoculated with homogenized mycelium of Laccaria bicolor and harvested at 15dpi. Total RNA was extracted and used for cDNA synthesis with SMART PCR cDNA synthesis kit (Clontech, USA).
Extracted molecule total RNA
Label Cy3
Label protocol The cDNA generated from the roots was labelled using a Klenow method following the protocol from North Carolina State University (van Zyl, U.S. Provisional Patent Application Nos. 60/372,872 and 60/390,142).
 
 
Hybridization protocol Hybridization and stringency washes were done according to the protocol from North Carolina State University (van Zyl, U.S. Provisional Patent Application Nos. 60/372,872 and 60/390,142).
Description rep A Pathogen (Cy5) vs. Mycorrhiza (Cy3) (12780946)
Data processing Raw intensity generated with QuantArray and statistically analysed using 2-interconnected mixed linear model approach.
 
Submission date Jul 28, 2006
Last update date Jul 31, 2006
Contact name Chris Smith
Organization name NCSU
Department Bioinformatics Research Center
Lab 1500 Partners II
Street address 840 Main Campus Dr
City Raleigh
State/province NC
ZIP/Postal code 27606
Country USA
 
Platform ID GPL4039
Series (2)
GSE5407 Comparative transcript profiling of interaction events in Pinus sylvestris root tissues following challenge (15dpi).
GSE5410 Comparative transcriptome analysis of early interaction events in Scots pine root tissues following challenge

Data table header descriptions
ID_REF Spot number on the array.
VALUE Ratio of normalized values.
CH1_NORM Normalized log2 channel 1 value
CH2_NORM Normalized log2 channel 2 value
CH1_RAW Raw channel 1 value
CH2_RAW Raw channel 2 value

Data table
ID_REF VALUE CH1_NORM CH2_NORM CH1_RAW CH2_RAW
1 0.9540416158926 -2.38803 -2.27828 9.766018 10.11937
2 1.001900572693 2.379809 2.384332 14.53386 14.78198
3 -0.34205771465155 -0.42173 0.144256 11.73232 12.54191
4 0.34135886753259 1.71378 0.585014 13.86783 12.98267
5 0.92941638376584 -2.95451 -2.74597 9.199542 9.651682
6 0.64871390558786 -1.0147 -0.65825 11.13935 11.7394
7 0.97856204611069 2.027339 1.983877 14.18139 14.38153
8 1.0932132047631 1.720046 1.880377 13.8741 14.27803
9 0.74643075522461 2.94376 2.197313 15.09781 14.59496
10 0.77278778990742 1.938593 1.498121 14.09264 13.89577
11 0.59706080603999 1.373778 0.820229 13.52783 13.21788
12 1.3420330800126 2.018258 2.708569 14.17231 15.10622
13 1.1719705376998 0.700149 0.820554 12.8542 13.21821
14 2.0461117646718 0.172559 0.353075 12.32661 12.75073
15 1.2959147330792 1.137135 1.47363 13.29118 13.87128
16 -0.089147706362436 0.692895 -0.06177 12.84694 12.33589
17 0.99925692196315 -3.66045 -3.65773 8.4936 8.739924
18 0.68065628343835 -0.67288 -0.458 11.48117 11.93965
19 0.76205298540831 1.393327 1.061789 13.54738 13.45944
20 0.96348410862675 -0.46692 -0.44987 11.68713 11.94778

Total number of rows: 5989

Table truncated, full table size 332 Kbytes.




Supplementary file Size Download File type/resource
GSM123809.txt.gz 689.7 Kb (ftp)(http) TXT

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