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Sample GSM301560 Query DataSets for GSM301560
Status Public on Jul 01, 2008
Title Treated leaf (3)
Sample type RNA
 
Source name Sugarcane (Saccharum spp. hybrids) leaf tissue
Organism Saccharum hybrid cultivar N19
Characteristics Hybrid cultivar N19
Biomaterial provider South African Sugarcane 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 20.3359 P 0.000445901
AFFX-BioB-M_at 21.6661 P 8.14279e-05
AFFX-BioB-3_at 19.1109 P 4.42873e-05
AFFX-BioC-5_at 16.7429 P 0.000340305
AFFX-BioC-3_at 18.5759 P 4.42873e-05
AFFX-BioDn-5_at 158.273 P 4.42873e-05
AFFX-BioDn-3_at 334.166 P 6.02111e-05
AFFX-CreX-5_at 918.34 P 5.16732e-05
AFFX-CreX-3_at 1188.72 P 4.42873e-05
AFFX-DapX-5_at 156.165 P 4.42873e-05
AFFX-DapX-M_at 254.434 P 5.16732e-05
AFFX-DapX-3_at 304.001 P 4.42873e-05
AFFX-LysX-5_at 17.438 P 4.42873e-05
AFFX-LysX-M_at 18.5203 P 0.000126798
AFFX-LysX-3_at 50.4217 P 4.42873e-05
AFFX-PheX-5_at 30.5961 P 5.16732e-05
AFFX-PheX-M_at 33.7795 P 4.42873e-05
AFFX-PheX-3_at 31.386 P 4.42873e-05
AFFX-ThrX-5_at 37.0087 P 0.000195116
AFFX-ThrX-M_at 48.4726 P 5.16732e-05

Total number of rows: 8387

Table truncated, full table size 320 Kbytes.




Supplementary file Size Download File type/resource
GSM301560.CEL.gz 984.1 Kb (ftp)(http) CEL
GSM301560.CHP.gz 44.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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