NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM88843 Query DataSets for GSM88843
Status Public on Dec 24, 2005
Title 50
Sample type RNA
 
Channel 1
Source name TO1
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 ME1
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 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 GPL1991
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
102435 0.526 270 266 319 390 396 362 B
102436 0.202 40391 45182 356 46476 41548 421 B
102437 null 0 519 362 0 568 398 X
102438 -0.534 256 230 317 177 197 343 B
102439 0.506 741 746 318 1055 1048 355 B
102440 -0.736 342 324 312 206 217 344 B
102441 -0.043 964 969 308 937 932 328 B
102442 -0.666 1375 1380 314 871 868 328 B
102443 0.239 2418 2391 328 2847 2880 327 B
102444 1.029 4039 4120 346 8244 8083 348 B
102445 -0.028 27148 29664 380 26481 24235 370 B
102446 0.163 4698 4761 348 5284 5214 344 B
102447 null 0 105 317 0 264 327 X
102448 0.791 12471 13313 339 21536 20175 346 B
102449 0.731 287 286 338 477 479 300 B
102450 0.444 546 553 312 741 732 310 B
102451 null 0 64 313 0 129 321 X
102452 0.322 389 388 309 488 490 328 B
102453 null 250 234 308 251 268 319 B
102454 -0.268 29679 32439 347 24545 22457 316 B

Total number of rows: 32448

Table truncated, full table size 1204 Kbytes.




Supplementary data files not provided

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