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Sample GSM237686 Query DataSets for GSM237686
Status Public on Mar 01, 2008
Title maize_root_region1_ws-ww_rep1-slideA
Sample type RNA
 
Channel 1
Source name maize root region1 water stress 48h rep 1
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 1
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 (GPL1990) 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 1st 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 15, 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 GPL1990
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
69987 0.155 3868 3736
69988 -0.228 6525 8479
69989 -0.428 36750 52001
69990 -0.324 2128 2812
69991 -0.355 16841 24622
69992 0.520 1067 783
69993 -0.002 552 600
69994 0.271 1823 1573
69995 -0.103 1350 1509
69996 -0.023 545 601
69997 0.856 51096 30168
69998 -0.185 24047 31021
69999 0.113 3132 3087
70000 -0.034 396 452
70001 0.178 2930 2751
70002 0.051 54905 53924
70003 -0.176 2982 3600
70004 -0.009 1286 1348
70005 -0.187 10154 13054
70006 -0.438 282 432

Total number of rows: 32448

Table truncated, full table size 716 Kbytes.




Supplementary file Size Download File type/resource
GSM237686.gpr.gz 4.3 Mb (ftp)(http) GPR
Processed data included within Sample table

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