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Sample GSM123827 Query DataSets for GSM123827
Status Public on Jul 31, 2006
Title 15dpi rep A Saprotroph (Cy5) vs. Mycorrhiza (Cy3) (12784934)
Sample type RNA
 
Channel 1
Source name Pinus sylvestris root tissues rep A Saprotroph (Cy5)
Organism Pinus sylvestris
Characteristics Pinus sylvestris roots challenged for 15 days with: Saprotroph (Trichoderma aureoviride)
Treatment protocol Pinus sylvestris seedlings (14 days post-germination) were inoculated with homogenized mycelium of Trichoderma aureoviride 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 Saprotroph (Cy5) vs. Mycorrhiza (Cy3) (12784934)
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 0.84003087029093 -2.78585 -2.3402 9.317413 10.12284
2 1.2156458184364 1.819451 2.211808 13.92272 14.67485
3 0.84638023344751 -1.20284 -1.01806 10.90043 11.44498
4 0.39688470241541 -0.19003 -0.07542 11.91324 12.38762
5 0.93061134258565 -2.66888 -2.48369 9.434384 9.979349
6 0.67709715177526 -1.0252 -0.69416 11.07807 11.76888
7 1.1102269572918 1.740019 1.931816 13.84329 14.39485
8 1.0989613984111 1.740032 1.912228 13.8433 14.37527
9 0.92669872192706 2.457215 2.277098 14.56048 14.74014
10 1.042865319781 1.637011 1.707182 13.74028 14.17022
11 1.329498309734 0.497259 0.661105 12.60053 13.12414
12 0.99236001189621 2.733643 2.712758 14.83691 15.1758
13 1.1957584412691 1.086063 1.298669 13.18933 13.76171
14 1.5629004113331 0.399433 0.624274 12.5027 13.08731
15 1.1489419836484 1.654275 1.900666 13.75754 14.3637
16 -0.099178660236606 -0.13271 0.013162 11.97055 12.4762
17 0.86009693920135 -3.35468 -2.88535 8.748585 9.57769
18 0.78000135676006 -0.73705 -0.5749 11.36622 11.88814
19 1.2918155256954 0.553096 0.714498 12.65636 13.17754
20 0.65026628430971 -0.4882 -0.31746 11.61507 12.14558

Total number of rows: 6144

Table truncated, full table size 342 Kbytes.




Supplementary file Size Download File type/resource
GSM123827.txt.gz 812.8 Kb (ftp)(http) TXT

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