NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM88836 Query DataSets for GSM88836
Status Public on Dec 24, 2005
Title 47
Sample type RNA
 
Channel 1
Source name ST1
Organism Zea mays
Characteristics Zea mays, Leaf, Development
Treatment protocol Stress
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 BS1
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 GPL1990
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
69987 -0.453 1063 1182 311 779 700 377 B
69988 null 0 173 321 0 209 370 M
69989 0.263 772 853 310 927 839 346 B
69990 0.098 360 369 306 387 377 344 B
69991 0.111 207 201 307 224 230 360 B
69992 2.993 128 131 298 1019 996 354 B
69993 null 0 145 298 0 217 364 M
69994 0.379 47372 49721 312 61449 58545 367 B
69995 1.144 213 216 310 470 464 376 B
69996 null 0 23 302 0 76 374 X
69997 0.345 11011 11937 316 14026 12938 369 B
69998 0.411 3529 3913 303 4686 4227 354 B
69999 null 0 96 319 0 249 357 M
70000 null 0 29 301 0 105 333 X
70001 -0.395 172 155 297 131 146 341 B
70002 -0.689 17526 18951 306 10856 10040 362 B
70003 0.566 122 109 301 181 202 348 B
70004 0.367 416 434 293 536 514 350 B
70005 null 0 137 297 0 209 349 M
70006 null 0 119 304 0 135 360 M

Total number of rows: 32448

Table truncated, full table size 1139 Kbytes.




Supplementary data files not provided

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