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Sample GSM301553 Query DataSets for GSM301553
Status Public on Jul 01, 2008
Title Control leaf (2)
Sample type RNA
 
Source name Sugarcane (Saccharum spp. hybrids) leaf tissue
Organism Saccharum hybrid cultivar N19
Characteristics Hybrid cultivar N19
Biomaterial provider South African Research Institute (SASRI)
Treatment protocol Cold-girdles were attached to sugarcane leaves (n=4) for a period of 56 h prior to harvest. The girdle consisted of 0.75 cm (diameter) soft plastic tubing, firmly clamped around each leaf, approximately 30 cm from the leaf base. Cooled water maintained at 5oC was then pumped through the tubing using a Grant LTD6G cooling bath (Grant Instruments, Barrington, Cambridge, UK). At harvest, leaf samples were immediately frozen in liquid nitrogen (–196oC) and subsequently milled in an A11 Basic Analysis Mill (IKA, Staufen, Germany). Ground leaf tissue was stored at –80oC in 50 ml centrifuge tubes prior to analysis.
Growth protocol Twelve month-old field grown Saccharum spp. (L.) hybrid cv. N19 (N19) cultivated at Mount Edgecombe, KwaZulu-Natal (SASRI) were used in the study, which was conducted in November, 2006. Plants were grown on a 5 x 15 m plot located on a north-east facing slope with a gradient of ca. 10o.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the extraction protocol of Bugos et al. (1995). Total RNA was checked for quality and integrity using a
Bioanalyser 2100 and the NanoChip protocol according to the manufacturer’s
directions (Agilent Technologies, Palo Alto, CA, USA). Labelled target used in
hybridisations was generated from 15 μg of total RNA using the One-Cycle
Eukaryotic Target Labeling Assay.
Label biotin
Label protocol All labelling, hybridizations of biotinylated cRNA to the GeneChip Sugarcane
Genome Arrays (Affymetrix, Inc., Santa Clara, CA, USA) and data collection
were performed by the Australian Genome Research Facility (AGRF, Melbourne, VIC, Australia).
 
Hybridization protocol All labelling, hybridizations of biotinylated cRNA to the GeneChip Sugarcane
Genome Arrays (Affymetrix, Inc., Santa Clara, CA, USA) and data collection
were performed by the Australian Genome Research Facility (AGRF, Melbourne, VIC, Australia).
Scan protocol The scanner operating software, GCOS, converted the signal on each array
into a DAT file, which was then used to generate CEL and CHP files for analysis (Casu et al., 2007).
Description N/A
Data processing GeneSpring 7.3 (Agilent Technologies) was used for data analysis.
 
Submission date Jun 30, 2008
Last update date Apr 09, 2010
Contact name Alistair James McCormick
E-mail(s) alistair.mccormick@plants.ox.ac.uk
Organization name University of Oxford
Department Department of Plant Science
Street address South Parks Rd
City Oxford
ZIP/Postal code OX13RB
Country United Kingdom
 
Platform ID GPL3844
Series (1)
GSE11934 Differential expression of genes in the leaves of sugarcane in response to sugar accumulation

Data table header descriptions
ID_REF
VALUE MAS5.0-calculated signal intensity
ABS_CALL A qualitative indicator of probe set detection. P: present; A: absent; M: marginal
DETECTION P-VALUE A p-value indicating the significance of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 33.9639 P 0.000972149
AFFX-BioB-M_at 32.5092 P 0.000126798
AFFX-BioB-3_at 20.5634 P 0.00010954
AFFX-BioC-5_at 31.038 P 0.000169227
AFFX-BioC-3_at 32.383 P 6.02111e-05
AFFX-BioDn-5_at 215.327 P 4.42873e-05
AFFX-BioDn-3_at 508.598 P 7.00668e-05
AFFX-CreX-5_at 1382.82 P 5.16732e-05
AFFX-CreX-3_at 1740.95 P 4.42873e-05
AFFX-DapX-5_at 498.981 P 4.42873e-05
AFFX-DapX-M_at 736.225 P 5.16732e-05
AFFX-DapX-3_at 824.746 P 4.42873e-05
AFFX-LysX-5_at 55.8528 P 4.42873e-05
AFFX-LysX-M_at 67.8159 P 6.02111e-05
AFFX-LysX-3_at 166.659 P 4.42873e-05
AFFX-PheX-5_at 129.175 P 4.42873e-05
AFFX-PheX-M_at 129.45 P 5.16732e-05
AFFX-PheX-3_at 108.901 P 4.42873e-05
AFFX-ThrX-5_at 142.229 P 7.00668e-05
AFFX-ThrX-M_at 165.533 P 4.42873e-05

Total number of rows: 8387

Table truncated, full table size 318 Kbytes.




Supplementary file Size Download File type/resource
GSM301553.CEL.gz 968.6 Kb (ftp)(http) CEL
GSM301553.CHP.gz 44.9 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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