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Sample GSM123825 Query DataSets for GSM123825
Status Public on Jul 31, 2006
Title 15dpi rep A Pathogen (Cy5) vs. Control (Cy3) (12784921)
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 Control (Cy3)
Organism Pinus sylvestris
Characteristics Pinus sylvestris unchallenged (control)
Treatment protocol Pinus sylvestris seedlings (14 days post-germination) were mock-inoculated with sterile distilled water 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. Control (Cy3) (12784921)
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 1.2023932225546 -1.59116 -1.9132 9.963496 9.419557
2 1.1915971705593 2.126498 2.533929 13.68116 13.86669
3 1.2513797462234 -1.44773 -1.81166 10.10692 9.521099
4 -0.88111244930795 0.850232 -0.74915 12.40489 10.58361
5 1.2272005339497 -1.61813 -1.98577 9.936528 9.346985
6 0.93704998434728 -0.76664 -0.71838 10.78802 10.61438
7 0.97145021395957 1.937983 1.882654 13.49264 13.21541
8 1.0682527985192 1.670437 1.784449 13.2251 13.11721
9 0.69600068136054 3.510623 2.443396 15.06528 13.77615
10 0.73195984421154 2.240474 1.639937 13.79513 12.9727
11 0.58528121196876 1.129006 0.660786 12.68366 11.99354
12 1.5181556503099 2.139334 3.247842 13.69399 14.5806
13 1.0278130956051 1.223021 1.257037 12.77768 12.5898
14 1.5217937005319 0.234242 0.356468 11.7889 11.68923
15 1.399886841996 1.373301 1.922466 12.92796 13.25522
16 -0.093272790630622 1.130662 -0.10546 12.68532 11.2273
17 1.3259161905149 -1.97066 -2.61293 9.584003 8.719826
18 0.9107419982882 -1.06321 -0.96831 10.49145 10.36445
19 0.60920695500303 1.069561 0.651584 12.62422 11.98434
20 1.0731299533167 -0.46055 -0.49423 11.09411 10.83853

Total number of rows: 6144

Table truncated, full table size 340 Kbytes.




Supplementary file Size Download File type/resource
GSM123825.txt.gz 769.8 Kb (ftp)(http) TXT

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