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Sample GSM206301 Query DataSets for GSM206301
Status Public on Jun 27, 2008
Title Upper pulvinus 5 min polysomal RNA biorep 1
Sample type RNA
 
Source name upper pulvinus_5min_Polysomal RNA_biorep 1
Organism Zea mays
Characteristics Polysomal RNA extracted from upper pulvinus
Gravity stimulation for 5min
Treatment protocol Plants were gravity stimulated by turning the pots horizontally (90º reorientation). Harvesting of the most gravity competent pulvinus (second pulvinus above soil level) was done at the following time points: 2 min, 5 min, 15 min, 30 min and 60 min. The upper (slow elongation) and lower (fast elongation) halves of six pulvini were harvested per time point. Control plants were kept vertical (no gravity stimulation). Pulvini from the control plants were separated into left and right halves (simulating upper and lower harvesting of pulvini in the gravity stimulated plants).
Growth protocol Maize (Zea mays strain B73) plants were cultivated in soil using 20cm diameter pots (two plants per pot, 6 plants per time point). Greenhouse conditions were as follow: natural light, 30ºC day and 26ºC night temperatures. Plants were grown to an age of ~6 weeks.
Extracted molecule polyA RNA
Extraction protocol Pulvini tissue was immediately frozen in liquid nitrogen after harvesting in the greenhouse. The harvested pulvini samples were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitrogen. This frozen powder was separated into aliquots, one used for extraction of total RNA, the other for isolation of polysomes and subsequent extraction of polysomal RNA. Polyribosomes were harvested as described in Davies, E. and S. Abe (1995). (Methods for isolation and analysis of polyribosomes. Methods Cell Biol 50: 209-22). Total RNA and polysome associated RNA was extracted using a RNeasy Plant Mini Kit (Qiagen).
Label biotin
Label protocol Complimentary RNA (cRNA) was produced according to Affymetrix Eukaryotic one-cycle target labeling assay as specified in the GeneChip Expression Analysis Technical Manual.
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc.
Scan protocol Scanning of the Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc.
Description no additional info
Data processing Data extraction was also performed by Expression Analysis Inc. Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs. The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays. The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500. The scaling factor is unique to each hybridization reaction and is in general below 10
 
Submission date Jun 28, 2007
Last update date Aug 14, 2011
Contact name Henrietta Myburg
E-mail(s) cassi_myburg@ncsu.edu
Phone 919-515 2225
Organization name NC State University
Department Botany
Street address 42218 Gardner Hall
City Raleigh
State/province NC
ZIP/Postal code 27695
Country USA
 
Platform ID GPL4032
Series (1)
GSE8320 Transcriptional and translational gene regulation in the maize pulvinus

Data table header descriptions
ID_REF
VALUE GCOS signal
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
Zm.17271.6.S1_x_at 4249.5 P 0.0003
Zm.10811.1.A1_s_at 10470.1 P 0.0003
Zm.665.1.S1_at 12132.9 P 0.0003
Zm.17271.7.A1_x_at 5079.6 P 0.0003
Zm.4814.3.A1_at 7099.8 P 0.0003
Zm.6189.1.A1_a_at 10142.8 P 0.0003
Zm.7727.4.S1_s_at 12350.2 P 0.0003
Zm.9.1.A1_a_at 12323.5 P 0.0003
Zm.2321.3.A1_at 11769.3 P 0.0003
Zm.12132.3.S1_a_at 9667.3 P 0.0003
Zm.127.3.A1_a_at 13168.5 P 0.0003
Zm.13367.1.S1_at 10663.1 P 0.0002
Zm.8188.1.A1_at 8799.8 P 0.0003
Zm.6189.1.A1_x_at 9181.6 P 0.0003
Zm.4510.1.A1_a_at 12672.6 P 0.0003
Zm.6532.1.A1_at 9266.7 P 0.0003
Zm.2992.1.A1_at 11179.8 P 0.0003
Zm.6045.1.A1_a_at 10243.0 P 0.0003
Zm.14429.1.A1_a_at 6628.0 P 0.0003
Zm.3157.3.A1_at 9001.4 P 0.0003

Total number of rows: 17545

Table truncated, full table size 540 Kbytes.




Supplementary file Size Download File type/resource
GSM206301.CEL.gz 2.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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