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Sample GSM219017 Query DataSets for GSM219017
Status Public on May 19, 2011
Title Lower#2, L5N310.gpr
Sample type RNA
 
Channel 1
Source name lower CY5
Organism Eucalyptus nitens
Characteristics Age: 9 years
Extracted molecule total RNA
Extraction protocol Two nine-year-old Eucalyptus nitens trees, tree 347 and tree Tall6, growing in Canberra, Australia, were used as a source of biological material. RNA was isolated from xylem from the vertical main stem and from the upper and lower quarter of branches oriented at approximately 45° from vertical. A bark window approximately 400 x 60 mm was removed from the stem using a hammer and chisel and young xylem tissue scraped from the exposed wood. A nine-year-old E. grandis tree growing in the same orchard was used as a source of xylem tissue for RNA isolation and cDNA library construction. Tissues were placed on ice after harvesting and then frozen in liquid nitrogen and stored at -80ºC. For each tree, slides were hybridized with probes synthesized from vertical xylem and one or other of upper or lower branch xylem.
Label Cy5
Label protocol Glass slides were processed according to the TeleChem protocols. Cy3-and Cy5-labeled (Amersham Pharmacia) cDNA probes were generated using the two-step labelling method described by Schenk et al. (2000). Application of the probe to microarray slides, hybridization, and subsequent washes of the slides were performed according to Schenk et al. (2000).
 
Channel 2
Source name vertical CY3
Organism Eucalyptus nitens
Characteristics Age: 9 years
Extracted molecule total RNA
Extraction protocol Two nine-year-old Eucalyptus nitens trees, tree 347 and tree Tall6, growing in Canberra, Australia, were used as a source of biological material. RNA was isolated from xylem from the vertical main stem and from the upper and lower quarter of branches oriented at approximately 45° from vertical. A bark window approximately 400 x 60 mm was removed from the stem using a hammer and chisel and young xylem tissue scraped from the exposed wood. A nine-year-old E. grandis tree growing in the same orchard was used as a source of xylem tissue for RNA isolation and cDNA library construction. Tissues were placed on ice after harvesting and then frozen in liquid nitrogen and stored at -80ºC. For each tree, slides were hybridized with probes synthesized from vertical xylem and one or other of upper or lower branch xylem.
Label Cy3
Label protocol Glass slides were processed according to the TeleChem protocols. Cy3-and Cy5-labeled (Amersham Pharmacia) cDNA probes were generated using the two-step labelling method described by Schenk et al. (2000). Application of the probe to microarray slides, hybridization, and subsequent washes of the slides were performed according to Schenk et al. (2000).
 
 
Hybridization protocol Prehybridization of slides, application of the probe to the microarray slides, hybridisation, and subsequent washing steps were performed according to manufacturer's instructions (Corning Microarray Technology).
Scan protocol Microarrays were scanned with a GenePix TM4000A laser scanner (Axon Instruments, Inc, Foster City, CA). Spot intensities from scanned slides were quantified using GenePix Pro 3.0 software. Grids were predefined and manually adjusted to ensure optimal spot recognition. Spots with dust or locally high background were discarded. After opening the scanned image, loading GenePix setting file and GenePix array list file, the analysis was performed using the Analyze option of 1 GenePix Pro3.0, resulting in a GPR file of gene expression.
Description lower vs normal stem #2
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: false
Data processing Normalization Method: Limma PrintTipLoess Normalisation within arrays, Limma Quantile Normalisation between arrays. Ref: Smyth, G.K. 2004. Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments. Statistical Applications in Genetics and Molecular Biology. Vol. 3: Iss. 1, Article 3.
 
Submission date Aug 20, 2007
Last update date Aug 14, 2011
Contact name Andrew Spriggs
E-mail(s) andrew.spriggs@csiro.au
Phone 612-6246-5193
Organization name CSIRO Plant Industry
Department Bioinformatics Group
Street address GPO Box 1600
City Canberra
State/province ACT
ZIP/Postal code 2601
Country Australia
 
Platform ID GPL5755
Series (1)
GSE8816 EucalyptWood

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio of medians with flagged values removed
BACK_TRANSFORM_VALUE Ratio of medians defined as CH1 divided by CH2 back transformed from normalised log
CH1_FG Channel 1 median feature pixel intensity (635nm)
CH1_BG Channel 1 median feature background intensity
CH2_FG Channel 2 median feature pixel intensity (532nm)
CH2_BG Channel 2 median feature background intensity
RATIO Unnormalized, untransformed ratio of medians (Ch1/Ch2 in unswapped sample, Ch2/Ch1 in swapped sample)
FLAG the type of flag associated with a feature. 0 denotes satisfactory features, <0 denotes un-satisfactory features that were excluded from normalisation and analysis
UNF_VALUE Normalized log2 ratio of medians

Data table
ID_REF VALUE BACK_TRANSFORM_VALUE CH1_FG CH1_BG CH2_FG CH2_BG RATIO FLAG UNF_VALUE
SP0000431373 -0.1531562 0.8992809 3771.0 196.0 5698.0 184.0 0.6618112 0 -0.1531562
SP0000431374 -0.3295539 0.7957825 6372.0 212.0 9990.0 204.0 0.6378378 0 -0.3295539
SP0000431375 0.0969923 1.0695414 3051.0 200.0 3126.0 213.0 0.9760077 0 0.0969923
SP0000431376 0.2043169 1.1521407 4040.0 197.0 3834.0 220.0 1.0537298 0 0.2043169
SP0000431377 0.1903226 1.1410188 3941.0 218.0 4029.0 220.0 0.9781584 0 0.1903226
SP0000431378 0.148583 1.1084802 3966.0 204.0 3807.0 223.0 1.0417652 0 0.148583
SP0000431379 0.5360959 1.4500432 9057.0 334.0 5911.0 290.0 1.532228 0 0.5360959
SP0000431380 0.5651722 1.4795641 12587.0 232.0 7976.0 226.0 1.5781093 0 0.5651722
SP0000431381 0.1119882 1.0807166 8759.0 219.0 8829.0 212.0 0.9920716 0 0.1119882
SP0000431382 0.2141843 1.1600478 5935.0 228.0 5412.0 231.0 1.0966371 0 0.2141843
SP0000431383 0 1 10969.0 274.0 9072.0 279.0 1.2091049 0 0
SP0000431384 0.031947 1.0223909 10846.0 319.0 8798.0 303.0 1.2327802 0 0.031947
SP0000431385 1.0560422 235.0 219.0 216.0 202.0 1.087963 -50 0.0786674
SP0000431386 1 203.0 213.0 217.0 200.0 0.9354839 -50 0
SP0000431387 0.4907026 1.405129 6670.0 254.0 5063.0 263.0 1.3174008 0 0.4907026
SP0000431388 0.4352289 1.3521253 7407.0 267.0 5790.0 267.0 1.2792746 0 0.4352289
SP0000431389 0.0450217 1.0316987 539.0 218.0 498.0 205.0 1.0823293 0 0.0450217
SP0000431390 0 1 377.0 237.0 388.0 215.0 0.9716495 0 0
SP0000431391 -0.395109 0.7604319 7245.0 252.0 8189.0 233.0 0.8847234 0 -0.395109
SP0000431392 -0.3594843 0.7794431 10499.0 251.0 12700.0 270.0 0.8266929 0 -0.3594843

Total number of rows: 9984

Table truncated, full table size 759 Kbytes.




Supplementary file Size Download File type/resource
GSM219017.gpr.gz 143.2 Kb (ftp)(http) GPR
Processed data included within Sample table

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