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Sample GSM237808 Query DataSets for GSM237808
Status Public on Mar 01, 2008
Title maize_root_region1_ww-ws_rep3-slideA
Sample type RNA
 
Channel 1
Source name maize root region1 control 48h rep 3
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 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 water stress 48h rep 3
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 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 3rd 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 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 0.090 2640 2360
69988 -0.098 5094 4983
69989 -0.040 27279 24895
69990 0.256 1561 1307
69991 0.033 12596 10834
69992 -0.524 678 1049
69993 -0.164 391 544
69994 0.083 1048 1029
69995 -0.027 1222 1266
69996 0.054 402 487
69997 0.512 43363 27542
69998 0.137 26861 21531
69999 0.093 2789 2480
70000 0.161 364 425
70001 0.091 2457 2205
70002 0.067 49498 43699
70003 0.135 2604 2260
70004 0.025 1224 1225
70005 0.135 8198 6691
70006 -0.255 243 407

Total number of rows: 32448

Table truncated, full table size 700 Kbytes.




Supplementary file Size Download File type/resource
GSM237808.gpr.gz 4.2 Mb (ftp)(http) GPR
Processed data included within Sample table

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