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Sample GSM206296 Query DataSets for GSM206296
Status Public on Jun 27, 2008
Title Lower pulvinus 15 min total RNA biorep 1
Sample type RNA
 
Source name lower pulvinus_15min_Total RNA_biorep 1
Organism Zea mays
Characteristics Total RNA extracted from lower pulvinus
Gravity stimulation for 15min
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 total 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 11545.6 P 0.0003
Zm.10811.1.A1_s_at 13184.3 P 0.0003
Zm.665.1.S1_at 13759.4 P 0.0003
Zm.17271.7.A1_x_at 13037.9 P 0.0003
Zm.4814.3.A1_at 12542.9 P 0.0003
Zm.6189.1.A1_a_at 11900.6 P 0.0003
Zm.7727.4.S1_s_at 12137.7 P 0.0003
Zm.9.1.A1_a_at 9605.9 P 0.0003
Zm.2321.3.A1_at 12235.8 P 0.0003
Zm.12132.3.S1_a_at 12171.6 P 0.0003
Zm.127.3.A1_a_at 7331.3 P 0.0003
Zm.13367.1.S1_at 12197.2 P 0.0002
Zm.8188.1.A1_at 9645.2 P 0.0003
Zm.6189.1.A1_x_at 11612.6 P 0.0003
Zm.4510.1.A1_a_at 11171.5 P 0.0003
Zm.6532.1.A1_at 11942.2 P 0.0003
Zm.2992.1.A1_at 10898.8 P 0.0003
Zm.6045.1.A1_a_at 11275.2 P 0.0003
Zm.14429.1.A1_a_at 10741.1 P 0.0003
Zm.3157.3.A1_at 10804.5 P 0.0003

Total number of rows: 17545

Table truncated, full table size 541 Kbytes.




Supplementary file Size Download File type/resource
GSM206296.CEL.gz 2.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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