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Sample GSM180285 Query DataSets for GSM180285
Status Public on Oct 31, 2008
Title OAR27K 720, 2/23/06
Sample type RNA
 
Channel 1
Source name EXP
Organism Arabidopsis thaliana
Characteristics Roots of Centaurea maculosa grown in competition with Festcua idahoensis
Biomaterial provider Callaway, University of Montana, Missoula
Treatment protocol Grown in competition with weak competitor, Festuca
Growth protocol In April 2005, 1.5 liters of sterile 20/30 grit sand (Lane Mountain, Inc. Valley, WA) was added to the bottom of 2.4 liter pots and 1 liter of weed-free sifted soil collected in Missoula, MT was placed on top of the sand. The pots were placed in a naturally lit greenhouse supplemented with artificial light and seeded with five seeds of Gaillardia aristata (strong competitor) or Festuca idahoensis (weak competitor), species which are both native to North American rangelands invaded by Centaurea. Once seedlings were established they were thinned to one plant per pot. After the natives had grown for 30 days, a single Centaurea seed collected from an invasive population in Missoula, MT was added to each pot containing native species and allowed to establish. Centaurea seeds were also grown in pots without natives. Plants were fertilized every three weeks with 100 mL of Miracle GrowTM solution per pot (0.34 grams 15-2-20 Miracle GrowTM per liter water), watered to near saturation, and rotated on the bench every 10 days. Plants were harvested in September of 2005, when native plants were approximately 153 days old and C. maculosa plants were 123 days old.
Extracted molecule total RNA
Extraction protocol RNeasy kit (quiagen)
Label CY5
Label protocol Genisphere Array900
 
Channel 2
Source name REF
Organism Arabidopsis thaliana
Characteristics Roots of Centaurea maculosa grown alone
Treatment protocol Centaurea maculosa grown in isolation
Growth protocol In April 2005, 1.5 liters of sterile 20/30 grit sand (Lane Mountain, Inc. Valley, WA) was added to the bottom of 2.4 liter pots and 1 liter of weed-free sifted soil collected in Missoula, MT was placed on top of the sand. The pots were placed in a naturally lit greenhouse supplemented with artificial light and seeded with five seeds of Gaillardia aristata (strong competitor) or Festuca idahoensis (weak competitor), species which are both native to North American rangelands invaded by Centaurea. Once seedlings were established they were thinned to one plant per pot. After the natives had grown for 30 days, a single Centaurea seed collected from an invasive population in Missoula, MT was added to each pot containing native species and allowed to establish. Centaurea seeds were also grown in pots without natives. Plants were fertilized every three weeks with 100 mL of Miracle GrowTM solution per pot (0.34 grams 15-2-20 Miracle GrowTM per liter water), watered to near saturation, and rotated on the bench every 10 days. Plants were harvested in September of 2005, when native plants were approximately 153 days old and C. maculosa plants were 123 days old.
Extracted molecule total RNA
Extraction protocol RNeasy kit (quiagen)
Label CY3
Label protocol Genisphere Array900
 
 
Hybridization protocol Genisphere Array900
Scan protocol Axon GenePix3.0
Description OAR27K 720, 2/23/06
Data processing GenePix Pro (gpr) and image files for each experiment were uploaded to a secure site through the Yale server where they could be accessed for analysis (http://ymd.med.yale.edu/ymd_prod/cgi-bin/gz_login.cgi). In the preliminary experiment, all unflagged genes were considered in the analysis without analyzing up or down regulation between tissues, to get a general overview of hybridization. For each chip, flagged genes were removed from the analysis. The average background was calculated for each dye channel (wavelength 635 and 532) and only genes having pixel counts (median minus background) over two times the average background in at least one channel were considered. In Experiment 2 each chip was initially analyzed separately. Flagged values and all channel values that were less than two standard deviations above the mean background were removed from the analysis. Ratios ((F635-B635)/(F532-B532)) of the remaining values were averaged per chip, and a correction factor was calculated for each chip, in order to set the average of all ratios equal to one. Ratios were multiplied by the appropriate correction factor to globally normalize the data. We chose oligos (array spots) that were present in all four chips for further analysis. This raises our confidence in the data, and allows us to compare the two experimental conditions. In addition, normalization provided better agreement between results from the microarray and those obtained by RT-PCR. Replicates (two per experimental condition) were combined and the average ratios and respective standard deviations were calculated for each oligo. A one sample t-test was preformed to identify oligos in which the test condition (Centaurea-Gaillardia or Centaurea-Festuca) was significantly different from the control (Centaurea alone). A two sample t-test was preformed to identify oligos that were differentially regulated between experiments (Centaurea-Gaillardia and Centaurea-Festuca). Accession numbers for each gene fitting the above criteria were used to query the TAIR (www.arabidopsis.org) database to determine function, and genes were then grouped into functional categories based on the Kyoto Encyclopedia of Genes and Genomics (KEGG) Orthology System (www.genome.jp/kegg/brite.html).
 
Submission date Apr 03, 2007
Last update date Jul 24, 2008
Contact name Amanda Broz
E-mail(s) akbroz@lamar.colostate.edu
Phone 970-491-4266
Organization name Colorado State University
Department Horticulture and Lanscape Architecture
Lab Jorge Vivanco
Street address 1173 Campus Delivery
City Fort Collins
State/province CO
ZIP/Postal code 80523
Country USA
 
Platform ID GPL988
Series (1)
GSE7444 Molecular response of an invasive weed to different competitive conditions.

Data table header descriptions
ID_REF Identifier reference, ID from the platform id
VALUE log2 (CY5/CY3); exp/ref)
CH1I_MEDIAN F532 Median: median feature pixel intensity at wavelength (532 nm)
CH1B_MEDIAN B532 Median: median feature background intensity at wavelength (532 nm)
CH2I_MEDIAN F635 Median: median feature pixel intensity at wavelength (635 nm)
CH2B_MEDIAN B635 Median: median feature background intensity at wavelength (635 nm)

Data table
ID_REF VALUE CH1I_MEDIAN CH1B_MEDIAN CH2I_MEDIAN CH2B_MEDIAN
3203159 -2.059 800 375 427 325
3203163 -5.755 818 386 342 334
3203165 -1.922 640 405 393 331
3203167 -4.239 712 391 359 342
3203169 -2.034 583 370 385 333
3203171 -2.286 713 357 406 333
3203173 -3.360 678 370 368 338
3203175 -2.518 808 390 409 336
3203177 -3.281 874 359 400 347
3203179 -3.094 689 356 367 328
3203181 -2.713 801 355 394 326
3203183 -3.087 702 362 384 344
3203187 -2.571 680 371 399 347
3203189 -2.569 718 350 408 346
3203191 -2.745 764 355 402 341
3203193 -3.536 845 381 380 340
3203195 -2.338 832 372 442 351
3203197 -3.773 785 375 386 356
3203199 -3.608 813 374 384 348
3203201 -4.745 788 359 358 342

Total number of rows: 15534

Table truncated, full table size 469 Kbytes.




Supplementary file Size Download File type/resource
GSM180285.txt.gz 2.7 Mb (ftp)(http) TXT

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