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Sample GSM88833 Query DataSets for GSM88833
Status Public on Dec 24, 2005
Title 62
Sample type RNA
 
Channel 1
Source name ME4
Organism Zea mays
Characteristics Zea mays, Leaf, Development
Treatment protocol Mesophyll prep
Growth protocol 10 days, 16h Light:8h Dark, 500umol m-2 s-1 light, 28C
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name BS4
Organism Zea mays
Characteristics Zea mays, Leaf, Development
Treatment protocol Bundle sheath prep
Growth protocol 10 days, 16h Light:8h Dark, 500umol m-2 s-1 light, 28C
Extracted molecule total RNA
Label Cy5
 
 
Description A number of taxa utilize C4 photosynthesis, to limit the impact of photorespiration upon photosynthetic performance. In order to achieve a local elevation of CO2 concentration, maize plants possess two photosynthetic cell types. Rubisco accumulation is restricted to bundle sheath (BS) cells that surround the leaf veins. Carbon fixation occurs initially in adjacent mesophyll (ME) cells. C4 compounds are transported into the BS cells where they are subsequently decarboxylated, releasing CO2. Although the major components of the C4 pathway have been well characterized, less is known about further metabolic partitioning in the maize leaf. Microarray hybridizations have been performed in order to further investigate metabolic differences between BS and ME cell types. BS strands and ME protoplasts were isolated from the leaves of 10 day old maize seedlings by mechanical disruption and enzymatic digestion respectively. To control for differences arising from these different protocols, total leaf (TO) and total leaf stress (ST) samples were also isolated. The ST sample was subjected to the same treatments as the ME sample, with the omission of cell-wall degrading enzymes. Leaves for the TO sample were harvested as for the BS strand sample. An interwoven loop design was used to compare the four treatment groups. A biological group consisted of a growth of plants from which pooled individuals were taken for the four treatments. Six biological replicates (groups) were used. Labeling was performed using the Genisphere Array 900-MPX kit according to the manufacturer's protocol. Post hybridization washes were performed according to the recommendations of the Maize Oligo Array Project. Scan settings were used for detection of moderate to high expression signals (gain ~ 60%. power 90%). Following hybridization with TO cDNA, ~1/3 of features provided signal above twice background and below saturation.
Data processing The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.
 
Submission date Dec 21, 2005
Last update date Dec 21, 2005
Contact name Ruairidh J Sawers
E-mail(s) rjs47@cornell.edu
Organization name Boyce Thompson Institute
Lab Bruntell
Street address Tower Rd
City Ithaca
State/province NY
ZIP/Postal code 14850
Country USA
 
Platform ID GPL1993
Series (1)
GSE3890 Gene expression profiling of bundle sheath and mesophyll cell types of wild-type maize seedlings.

Data table header descriptions
ID_REF Spot identifier for each feature
VALUE Normalized log2 ratio of normalized intensities defined by CH2/CH1. This value is set to null if it is flagged with "M" or "X"
CH1_NORMALIZED Normalized background subtracted CH1 intensity (RED channel)
CH1_RAW Background (CH1_BACKGROUND) subtracted raw intensity (F635 Mean - B635 Media)
CH1_BACKGROUND CH1 background median intensity (B635 Media)
CH2_NORMALIZED Normalized background subtracted CH2 intensity (GREEN channel)
CH2_RAW Background (CH2_BACKGROUND) subtracted raw intensity (F532 Mean - B532 Media)
CH2_BACKGROUND CH2 background median intensity (B532 Media)
FLAG B: no flag, good spot; X: undetectable spot; M: flagged for diameter < 70 microns, the percentage of saturated pixels > 30% or not validated PCR product

Data table
ID_REF VALUE CH1_NORMALIZED CH1_RAW CH1_BACKGROUND CH2_NORMALIZED CH2_RAW CH2_BACKGROUND FLAG
167331 0.678 503 469 448 807 865 1226 B
167332 0.356 37216 38469 476 47453 45907 1272 B
167333 null 0 183 460 0 152 1245 X
167334 null 0 123 422 0 314 1166 X
167335 -0.836 2571 2509 431 1429 1464 1134 B
167336 null 0 130 437 0 167 1199 X
167337 -0.268 1551 1506 431 1289 1327 1206 B
167338 -0.376 3707 3850 435 2836 2731 1219 B
167339 0.799 3023 3158 446 5272 5047 1276 B
167340 -0.785 32844 34342 467 19125 18291 1174 B
167341 -1.088 27323 28728 452 12895 12264 1215 B
167342 -0.81 8678 9178 421 4961 4691 1062 B
167343 null 0 84 410 0 76 1045 X
167344 -0.321 27675 28944 422 22088 21120 1188 B
167345 null 0 15834 493 0 20162 1284 M
167346 0.536 1042 1013 430 1511 1554 1096 B
167347 null 0 53 404 0 86 1114 X
167348 0.333 1708 1667 413 2159 2212 1117 B
167349 null 0 100 415 0 123 1089 X
167350 -0.073 5169 5409 395 4920 4701 1099 B

Total number of rows: 32448

Table truncated, full table size 1142 Kbytes.




Supplementary data files not provided

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