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Sample GSM245934 Query DataSets for GSM245934
Status Public on Apr 03, 2008
Title Leaf_Water Control_Rep 2_48 h After Treatment
Sample type RNA
 
Source name First trifoliolate leaf, 48h after sprayed with water control
Organism Glycine max
Characteristics Soybean cv. OAC Bayfield, V1 stage of development, first trifoliolate leaf.
Treatment protocol Once the soybean plants had reached the V1 stage of development, the first trifoliolate leaf of each plant was sprayed with 2 mL of sterilized dH2O, containing 0.02% Tween 20. 48 h later, the first trifoliolate leaf was harvested, immediately submerged in liquid N2, and stored at -80 ºC until extraction. Water CONTROL, 2 of 3 replicates.
Growth protocol Soybean cultivar (cv.) Ontario Agricultural College (OAC) Bayfield seeds were surface-sterilized in 25% v/v sodium hypochlorite (Javex) for 2 min and then washed five times with distilled water (dH2O). The seeds were then spread evenly on a 5 cm thick bed of autoclaved vermiculite in a large plastic tray (54 x 28 x 6.5 cm) with holes at the bottom, to allow drainage of excess water, and then covered with 1 cm of vermiculite. The tray, with seeds, was placed in a growth chamber with a 16 h photoperiod (25 ºC) and an 8 h period of darkness (20 ºC). The germination/rooting medium was kept moist through regular additions of dH2O. When the cotyledons had emerged and separated (V1 growth stage) the seedlings were transferred to 5 cm pots containing a mixture of Pro-Mix (sphagnum peat moss) and perlite, as growth media. Each seedling was transferred to an individual pot and returned to the growth chamber under the conditions described above. The seedlings were watered with ½ strength Hoagland’s solution every day.
Extracted molecule total RNA
Extraction protocol Frozen leaf tissue was rapidly ground with a mortar and pestle chilled with liquid N2 that had been placed in a -20 ºC freezer for 4 h prior to RNA extraction. Total RNA was extracted from ~100 mg of finely-ground, frozen tissue using the Qiagen RNeasy® Plant Mini Kit for total RNA isolation, with an on-column DNase digestion via the RNase-free DNase Set, according to the manufacturer’s instructions. Samples were stored at -80 oC until use.
Label biotin
Label protocol 3.5 µg was used to synthesize labeled target cRNA using the GeneChip HT One-Cycle Target Labeling and Controls kit (Affymetrix). cRNA were labelled with biotin, stained with Streptavidin-phycoerythrin (SAPE) and detected with Biotinylated anti-streptavidin antibody.
 
Hybridization protocol The cRNA quality was determined using a 2100 BioAnalyzer equipped with an RNA Nano LabChip, overnight hybridization of the chip utilized 15 µg of fragmented cRNA and the staining and washes were performed using an Affymetrix GeneChip Fluidics Station 450 robot, following the manufacturer's protocols.
Scan protocol The microarray chips were scanned with an Affymetrix GeneChip Scanner 3000 7G, following the manufacturer's protocols.
Description All steps followed Affymetrix guidelines and protocols.
Data processing Robust multi-array average (RMA) analysis was performed on the .CEL files (with normalization and suppression of background noise). The base 2 logarithm of RMA signals were median-centered so that the median log-scale expression measure for each GeneChip was zero.
 
Submission date Nov 29, 2007
Last update date Aug 14, 2011
Contact name John K Lindsay
E-mail(s) john.lindsay@mcgill.ca
Phone 5143987851
Organization name McGill University
Department Plant Science
Street address 21111 Lakeshore Rd
City Ste.Anne-de-Bellevue
State/province Quebec
ZIP/Postal code H9X 3V9
Country Canada
 
Platform ID GPL4592
Series (1)
GSE9730 Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
AFFX-BioB-3_at 7.27733
AFFX-BioB-5_at 7.617212
AFFX-BioB-M_at 7.729567
AFFX-BioC-3_at 8.769621
AFFX-BioC-5_at 8.723606
AFFX-BioDn-3_at 11.39409
AFFX-BioDn-5_at 10.50555
AFFX-CreX-3_at 13.16371
AFFX-CreX-5_at 12.73733
AFFX-DapX-3_at 9.108772
AFFX-DapX-5_at 7.463743
AFFX-DapX-M_at 8.30245
AFFX-Gm_18SrRNA_at 5.236113
AFFX-Gm_Actin_3_at 8.459785
AFFX-Gm_Actin_5_at 3.092527
AFFX-Gm_Actin_M_at 6.663284
AFFX-Gm_GlutTrans_3_r_at 11.40902
AFFX-Gm_GlutTrans_5_s_at 11.25506
AFFX-Gm_GlutTrans_M_at 10.86383
AFFX-Gm_P450_3_s_at 9.243659

Total number of rows: 61170

Table truncated, full table size 1762 Kbytes.




Supplementary file Size Download File type/resource
GSM245934.CEL.gz 4.4 Mb (ftp)(http) CEL
GSM245934.CHP.gz 13.7 Mb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table

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