NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM219013 Query DataSets for GSM219013
Status Public on May 19, 2011
Title Lower #1, L3N514.gpr
Sample type RNA
 
Channel 1
Source name vertical 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 lower 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 #1
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: true
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 0.1185265 1.0856255 2405.0 800.0 3004.0 981.0 1.2490644 0 0.1185265
SP0000431374 0.3329344 1.2595727 3032.0 1288.0 4119.0 1574.0 1.3585092 0 0.3329344
SP0000431375 1.064885 2.0920031 1622.0 798.0 3341.0 821.0 2.0598027 0 1.064885
SP0000431376 1.001624 2.0022526 1889.0 1454.0 4056.0 1484.0 2.1471678 0 1.001624
SP0000431377 0.9279375 3273.0 2130.0 3281.0 2264.0 1.0024442 -50 -0.1079004
SP0000431378 -0.1487976 0.9020019 2941.0 922.0 2800.0 894.0 0.9520571 0 -0.1487976
SP0000431379 -0.3224744 0.7996971 4853.0 2668.0 3870.0 2878.0 0.7974449 0 -0.3224744
SP0000431380 -0.3112621 0.8059364 5430.0 2283.0 4496.0 2313.0 0.8279926 0 -0.3112621
SP0000431381 -0.0753442 0.9491157 8648.0 2661.0 5947.0 2725.0 0.6876735 0 -0.0753442
SP0000431382 -0.0557695 0.9620812 6744.0 1820.0 4664.0 2037.0 0.6915777 0 -0.0557695
SP0000431383 0.2012891 1.1497252 5321.0 2766.0 5721.0 3259.0 1.0751738 0 0.2012891
SP0000431384 0.3930135 1.3131334 5675.0 2514.0 6504.0 2915.0 1.1460793 0 0.3930135
SP0000431385 1.0530094 3232.0 3163.0 3674.0 3415.0 1.1367574 -50 0.0745183
SP0000431386 1 2573.0 2730.0 2730.0 2881.0 1.0610183 -50 0
SP0000431387 0.441419 1.3579393 4649.0 3059.0 6695.0 3497.0 1.4400946 0 0.441419
SP0000431388 1.022244 2.0310757 4938.0 3136.0 9931.0 3556.0 2.0111381 0 1.022244
SP0000431389 1.0379307 1215.0 1291.0 1424.0 1461.0 1.1720165 -50 0.0537102
SP0000431390 1 1452.0 1599.0 1729.0 1764.0 1.1907713 -50 0
SP0000431391 0 1 6306.0 1730.0 6118.0 1922.0 0.9701871 0 0
SP0000431392 0.0513293 1.0362193 7506.0 2019.0 7168.0 2193.0 0.9549694 0 0.0513293

Total number of rows: 9984

Table truncated, full table size 751 Kbytes.




Supplementary file Size Download File type/resource
GSM219013.gpr.gz 156.1 Kb (ftp)(http) GPR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap