NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM88847 Query DataSets for GSM88847
Status Public on Dec 24, 2005
Title 68
Sample type RNA
 
Channel 1
Source name TO6
Organism Zea mays
Characteristics Zea mays, Leaf, Development
Treatment protocol None
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 BS6
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 -0.088 191 154 293 179 222 317 B
167332 0.176 14616 12305 299 16524 19627 311 B
167333 null 0 106 295 0 226 300 M
167334 null 0 39 293 0 101 305 X
167335 -0.62 702 616 296 454 517 314 B
167336 null 0 10 300 0 175 307 M
167337 -0.043 357 300 295 348 414 314 B
167338 -0.453 1802 1590 296 1318 1494 311 B
167339 null 0 1379 300 0 2408 330 M
167340 -0.321 15914 13423 318 12794 15169 332 B
167341 -1.433 13844 11805 319 5169 6062 309 B
167342 -0.62 3922 3411 308 2554 2937 312 B
167343 null 0 118 302 0 246 310 M
167344 -0.251 13794 11664 306 11655 13784 325 B
167345 null 0 66 312 0 97 319 X
167346 -0.104 439 376 309 409 477 325 B
167347 null 0 13 300 0 32 323 X
167348 -0.251 668 588 295 563 639 306 B
167349 null 0 40 298 0 109 324 X
167350 null 0 3138 296 0 5515 332 M

Total number of rows: 32448

Table truncated, full table size 1122 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap