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Sample GSM219015 Query DataSets for GSM219015
Status Public on May 19, 2011
Title Upper #1, u5n321.gpr
Sample type RNA
 
Channel 1
Source name upper 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 upper vs normal stem #1
Biological Replicate: 1, Technical Replicate: 1, 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 -0.1154387 0.9231016 3944.0 148.0 5727.0 252.0 0.6886677 0 -0.1154387
SP0000431374 -0.2162998 0.8607703 8365.0 164.0 11227.0 268.0 0.7450788 0 -0.2162998
SP0000431375 -0.1894773 0.8769234 2216.0 153.0 3222.0 232.0 0.6877716 0 -0.1894773
SP0000431376 -0.2356106 0.8493255 3731.0 171.0 5300.0 260.0 0.7039623 0 -0.2356106
SP0000431377 0.2120621 1.1583427 1633.0 135.0 2244.0 230.0 0.7277184 0 0.2120621
SP0000431378 0.135997 1.0988519 1357.0 121.0 1944.0 212.0 0.6980453 0 0.135997
SP0000431379 0.0902782 1.0645754 1881.0 180.0 2277.0 240.0 0.826087 0 0.0902782
SP0000431380 0.0693946 1.0492763 2305.0 133.0 2809.0 246.0 0.8205767 0 0.0693946
SP0000431381 0.5341845 1.4481234 5784.0 192.0 4355.0 268.0 1.3281286 0 0.5341845
SP0000431382 0.6411075 1.5595259 6043.0 193.0 4050.0 251.0 1.4920988 0 0.6411075
SP0000431383 0.0133919 1.0093257 4343.0 197.0 4588.0 260.0 0.9465998 0 0.0133919
SP0000431384 -0.0731284 0.9505745 4538.0 197.0 5053.0 267.0 0.8980803 0 -0.0731284
SP0000431385 1.1253584 183.0 182.0 256.0 266.0 0.7148438 -50 0.1703845
SP0000431386 1.0408133 273.0 253.0 389.0 338.0 0.7017995 -50 0.0577113
SP0000431387 -0.0398912 0.9727283 3726.0 215.0 4868.0 289.0 0.7654067 0 -0.0398912
SP0000431388 -0.1484398 0.9022256 4445.0 193.0 6126.0 265.0 0.7255958 0 -0.1484398
SP0000431389 0.0783673 1.0558225 253.0 143.0 351.0 191.0 0.7207977 0 0.0783673
SP0000431390 -0.0391501 0.9732281 281.0 166.0 415.0 233.0 0.6771084 0 -0.0391501
SP0000431391 0.1143021 1.0824513 5272.0 186.0 4867.0 265.0 1.0832135 0 0.1143021
SP0000431392 0.0107883 1.0075059 5330.0 195.0 4983.0 252.0 1.0696368 0 0.0107883

Total number of rows: 9984

Table truncated, full table size 755 Kbytes.




Supplementary file Size Download File type/resource
GSM219015.gpr.gz 141.3 Kb (ftp)(http) GPR
Processed data included within Sample table

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