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Sample GSM123806 Query DataSets for GSM123806
Status Public on Jul 31, 2006
Title 15dpi rep A Control (Cy5) vs. Mycorrhiza (Cy3) (12770659)
Sample type RNA
 
Channel 1
Source name Pinus sylvestris root tissues rep A Control (Cy5)
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 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 Control (Cy5) vs. Mycorrhiza (Cy3) (12770659)
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 0.964551448081 -1.6988 -1.63858 10.86022 11.29192
2 0.90275566723174 2.440389 2.203075 14.99941 15.13358
3 1.1800050616538 -1.42246 -1.67851 11.13657 11.25199
4 1.5960713264041 -0.20974 -0.33476 12.34928 12.59575
5 0.99611244309413 -2.06042 -2.05241 10.49861 10.87809
6 0.78586912660354 -1.06561 -0.83743 11.49341 12.09308
7 1.0882875383031 1.580812 1.720378 14.13984 14.65088
8 0.9974499220439 1.499562 1.495738 14.05859 14.42624
9 0.91507564821153 2.655846 2.4303 15.21487 15.3608
10 0.96064784673869 1.651193 1.586215 14.21022 14.51672
11 0.44481858768786 0.31806 0.141479 12.87708 13.07198
12 0.91039094335268 2.842023 2.587352 15.40105 15.51785
13 0.90292150154599 0.85059 0.768016 13.40962 13.69852
14 0.4708306021163 -0.21358 -0.10056 12.34544 12.82994
15 0.85688326459848 1.774209 1.52029 14.33323 14.45079
16 1.0657223488549 -0.55278 -0.58911 12.00624 12.34139
17 0.82969931092798 -2.93293 -2.43345 9.626097 10.49706
18 1.1127816729781 -0.80013 -0.89037 11.7589 12.04013
19 0.70503176598443 0.704842 0.496936 13.26387 13.42744
20 1.1602266288952 -0.61775 -0.71673 11.94127 12.21377

Total number of rows: 6144

Table truncated, full table size 342 Kbytes.




Supplementary file Size Download File type/resource
GSM123806.txt.gz 846.3 Kb (ftp)(http) TXT

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