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Sample GSM237813 Query DataSets for GSM237813
Status Public on Mar 01, 2008
Title maize_root_region1_ws-ww_rep2-slideB
Sample type RNA
 
Channel 1
Source name maize root region1 water stress 48h rep 2
Organism Zea mays
Characteristics Region 1 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of low water potential.
Treatment protocol See the growth protocol.
Growth protocol Seeds were imbibed for 24 h in 1 mM CaSO4, then germinated for 28 h in vermiculite well-moistened with 1 mM CaSO4 at 29°C in the dark. Seedlings with primary roots 12-20 mm in length were transplanted into vermiculite mixed with pre-determined amounts of 1 mM CaSO4 to create either high (-0.03 MPa) or low (-1.6 MPa) water potential and grown under near-saturating humidity conditions to prevent further drying of the media. Root tips were collected at 48h after transplant to vermiculite of either high or low water potential.
Extracted molecule total RNA
Extraction protocol The apical 12 mm of each root was sectioned into three regions based on previously-characterized longitudinal expansion rate profiles: region 1, 0-3 mm plus the root cap; region 2, 3-7 mm; region 3, 7-12 mm. Samples were immediately frozen in liquid nitrogen. Total RNA was isolated using Trizol reagent following the manufacturer’s instructions (Invitrogen Corp., Carlsbad, CA). Residual DNA was removed by Dnase I (Invitrogen, Carlsbad, CA) treatment for 15 min at room temperature, followed by use of RNeasy columns (Qiagen, Valencia, CA).
Label Cy5
Label protocol First strand cDNAs were synthesized from 50 μg of total RNA using anchored oligo(dT)24 primers with SuperScript III RT (Invitrogen, Carlsbad, CA), and aminoallyl-dUTP was incorporated into the cDNAs. The RNA template was removed by treatment with RnaseH (Invitrogen, Carlsbad, CA), and cDNAs were purified to remove unincorporated aminoallyl-dUTP using Microcon 30 spin concentrators (Millipore Corp., Bedford, MA). Following purification, monoreactive-Cye5 or Cye3 dyes (Amersham Biosciences Corp., Piscataway, NJ) were conjugated to aminoallyl-dUTP on the cDNAs and the unconjugated dye was removed using Qiagen PCR purification columns.
 
Channel 2
Source name maize root region1 control 48h rep 2
Organism Zea mays
Characteristics Region 1 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of high water potential.
Treatment protocol See the growth protocol.
Growth protocol Seeds were imbibed for 24 h in 1 mM CaSO4, then germinated for 28 h in vermiculite well-moistened with 1 mM CaSO4 at 29°C in the dark. Seedlings with primary roots 12-20 mm in length were transplanted into vermiculite mixed with pre-determined amounts of 1 mM CaSO4 to create either high (-0.03 MPa) or low (-1.6 MPa) water potential and grown under near-saturating humidity conditions to prevent further drying of the media. Root tips were collected at 48h after transplant to vermiculite of either high or low water potential.
Extracted molecule total RNA
Extraction protocol The apical 12 mm of each root was sectioned into three regions based on previously-characterized longitudinal expansion rate profiles: region 1, 0-3 mm plus the root cap; region 2, 3-7 mm; region 3, 7-12 mm. Samples were immediately frozen in liquid nitrogen. Total RNA was isolated using Trizol reagent following the manufacturer’s instructions (Invitrogen Corp., Carlsbad, CA). Residual DNA was removed by Dnase I (Invitrogen, Carlsbad, CA) treatment for 15 min at room temperature, followed by use of RNeasy columns (Qiagen, Valencia, CA).
Label Cy3
Label protocol First strand cDNAs were synthesized from 50 μg of total RNA using anchored oligo(dT)24 primers with SuperScript III RT (Invitrogen, Carlsbad, CA), and aminoallyl-dUTP was incorporated into the cDNAs. The RNA template was removed by treatment with RnaseH (Invitrogen, Carlsbad, CA), and cDNAs were purified to remove unincorporated aminoallyl-dUTP using Microcon 30 spin concentrators (Millipore Corp., Bedford, MA). Following purification, monoreactive-Cye5 or Cye3 dyes (Amersham Biosciences Corp., Piscataway, NJ) were conjugated to aminoallyl-dUTP on the cDNAs and the unconjugated dye was removed using Qiagen PCR purification columns.
 
 
Hybridization protocol The purified Cy3 and Cy5-labeled cDNAs were concentrated to 60 μl and hybridized to the maize oligonucleotide array (GPL1991) for 16-18 h at 42 ºC. Following hybridization, the arrays were washed three times, twice with medium stringency buffer (1X SSC, 0.2% SDS) and once with high stringency buffer (0.1X SSC, 0.2% SDS).
Scan protocol Washed slides were dried and scanned immediately using a GenePix scanner (GenePix® 4000B, Axon Instruments, Inc.) at 532 nm (17 mW) and 635 nm (10 mW). GenePix Pro 4.1 software was then used to extract spot intensity data.
Description This is the 2nd of 4 biological replications, and one half of a dye-swap pair.
Data processing Mean signal intensities were used without background correction and data from all 8 chips (4 reps with dye-swap) were normalized using the Loess transformation.
 
Submission date Oct 16, 2007
Last update date Aug 14, 2011
Contact name William G. Spollen
E-mail(s) spollenw@missouri.edu
Phone 573-884-8151
Organization name University of Missouri-Columbia
Department Informatics Research Core Facility
Lab Scott A. Givan
Street address 113 Bond Life Sciences Center
City Columbia
State/province MO
ZIP/Postal code 65211
Country USA
 
Platform ID GPL1991
Series (2)
GSE9341 Gene expression in Maize root region 1 at low water potential
GSE9379 Gene expression in Maize root

Data table header descriptions
ID_REF
VALUE log2 ratio of mean intensities normalized across chips
CH1_SIG_MEAN raw mean intensity of F635
CH2_SIG_MEAN raw mean intensity of F532

Data table
ID_REF VALUE CH1_SIG_MEAN CH2_SIG_MEAN
102435 -0.130 339 413
102436 -0.405 13721 16515
102437 -0.225 409 518
102438 -0.325 286 401
102439 -0.109 1324 1378
102440 0.190 445 426
102441 -0.224 622 744
102442 -0.504 677 965
102443 -0.055 8158 7644
102444 -0.347 10477 12057
102445 -0.337 3607 4168
102446 -0.027 1463 1431
102447 -0.145 769 854
102448 -0.712 12531 18657
102449 -0.475 767 1060
102450 -0.218 632 752
102451 -0.334 190 238
102452 -0.906 835 1529
102453 -0.189 367 461
102454 -0.364 5061 5900

Total number of rows: 32448

Table truncated, full table size 728 Kbytes.




Supplementary file Size Download File type/resource
GSM237813.gpr.gz 2.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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