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Series GSE4276 Query DataSets for GSE4276
Status Public on Jan 01, 2007
Title Soybean cultivars OX951 & OX736, seed coat permeablity comparison
Organism Glycine max
Experiment type Expression profiling by array
Summary Soybean cultivars, OX951 & OX736, comparison of seed coat at 3 growth stages, early, mid & late
Keywords: time course
 
Overall design 26 microarray slides GPL3015; 2 soybean cultivars, OX951 (with impermeable seed coat) and OX736 (with permeable seed coat); 2 technical reps for each growth stage (dye swap);4 biological reps from 2 consecutive growing seasons, 2004 & 2005 (2 reps per year); 3 growth stages, early (E) 10 to 20 days after pollination (dap), mid (M) 21 to 35 dap and late (L) 36 to 50 dap; total RNA isolated from the whole seed for the early stage and seed coat only for the mid & late stages. The slide data was analyzed in GeneSpringGX7.3 Agilent Technologies, using background subtracted values. The ratio for OX736/OX951 was calculated from the 2 colour hybridization (same slide) and relative expression for seed coat development as a function of time was calculated using all the slides treated as single channel data.The slide identites are 2004 rep1 GSM97598 to 97603, 2004 rep 2 GSM97606 to 97611, 2005 rep3 GSM97612 to 97617, 2005 rep4 GSM97618 to 97623. Two self test slides were included for 2004 rep1 L stage, OX951/OX951 and OX736/OX736 , GSM907604-97605
 
Contributor(s) Gijzen M, Qutob D, Moy P
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Feb 20, 2006
Last update date May 19, 2012
Contact name Mark Gijzen
E-mail(s) gijzenm@agr.gc.ca
Phone 519-457-1470
Fax 519-457-3997
Organization name SCPFRC London
Department Agriculture & AgriFood Canada
Lab Plant Biochemistry
Street address 1391 Sandford St
City London
State/province ON
ZIP/Postal code N5V 4T3
Country Canada
 
Platforms (1)
GPL3015 Keck Glycine max 18kA cDNA Prints101-108
Samples (26)
GSM97598 #148933 Soybean seed coat, OX951 & OX736, 2004 rep1 time course
GSM97599 #148934 Soybean seed coat, OX951 & OX736, 2004 rep1 time course
GSM97600 #148935 Soybean seed coat, OX951 & OX736, 2004 rep1 time course
Relations
BioProject PRJNA94943

Table 1: Seed coat ratio results (Merged normalized data of the ratio, OX736 divided by OX951, 4 biological reps merged in GeneSpringGX7.3, full soybean data set, file prepared April 11th 2006, average raw data intensities are available from the GSE4276 SC developemnt full data set file, Gm-b10BB EST's had 4 replicate spots per array, these results are the average of 32 analyses) header descriptions
Group A, combined has 1460 EST's with 18 in both A1 & A2; A1, 666 EST's that are 1.5x up regulated OX736/OX951, filtered on minimum ratio of 1.5 in any time point; A2, 812 EST's that are 1.5x down regulated OX736/OX951, filtered on maximum ratio of 0.67 in any time point; B, 14223 EST's with little change in ratio (min 0.67 & max 1.5) but with raw data intensity >10; C, 2669 EST's with average background intensity <10 in all conditions
Systematic name
Genbank
OX736/OX951 (Early) Early development stage, 10 to 20 days after pollination (DAP)
OX736/OX951 (Mid) Mid development stage, 12 to 35 DAP
OX736/OX951 (Late) Late development stage, 36 to 50 DAP
Common name

Data table
Group Systematic name Genbank OX736/OX951 (Early) OX736/OX951 (Mid) OX736/OX951 (Late) Common name
B Gm-b10BB-1 AW318030 1.21 1.17 1.07 ELONGATION FACTOR 1-ALPHA
B Gm-b10BB-2 BE806777 1.1 1.04 0.92 PHENYLALANINE AMMONIA-LYASE 1
B Gm-b10BB-3 AI855764 1.19 1.17 1 CHALCONE SYNTHASE 1
B Gm-b10BB-4 AW707011 1.15 1.16 0.9 CHALCONE SYNTHASE 1
C Gm-b10BB-5 L03352 1.16 1.16 1.02 Glycine max chalcone synthase (chs6) gene, complete cds
B Gm-b10BB-6 AI437793 1.07 1.04 0.71 CHALCONE SYNTHASE 7
B Gm-b10BB-7 AI441937 1.09 1.06 0.75 CHS8 CHALCONE SYNTHASE 8
A2 Gm-b10BB-9 BG157194 1.04 0.65 0.81 CHALCONE--FLAVONONE ISOMERASE
A2 Gm-b10BB-10 BG157194 1.11 0.56 0.76 CHALCONE--FLAVONONE ISOMERASE
A2 Gm-b10BB-11 AI930858 1.08 0.59 0.79 CHALCONE ISOMERASE
B Gm-b10BB-12 AI900038 1.15 1.07 1.18 NARINGENIN,2-OXOGLUTARATE 3-DIOXYGENASE
B Gm-b10BB-13 AW277481 1.19 1.17 1.19 NARINGENIN,2-OXOGLUTARATE 3-DIOXYGENASE
A1 Gm-b10BB-14 AW156539 1.53 1.62 1.46 FLAVONOL SYNTHASE
B Gm-b10BB-15 BE059354 1.26 1.26 1.35 FLAVONOL SYNTHASE
A2 Gm-b10BB-17 AW830233 1.04 0.61 0.81 CYTOCHROME P450 71D9
A2 Gm-b10BB-18 AW569417 1.1 0.5 0.74 CYTOCHROME P450 71D8
C Gm-b10BB-19 BE805102 1.18 0.56 0.81 CYTOCHROME P450 71D8
B Gm-b10BB-20 BG157080 0.97 1.04 1.14 FLAVONOID 3', 5'-HYDROXYLASE LIKE PROTEIN.
C Gm-b10BB-21 BG041082 1.09 1.14 1.16 FLAVONOID 3', 5'-HYDROXYLASE-LIKE PROTEIN.
C Gm-b10BB-22 BF069512 1.1 1.05 1.13 FLAVONOID 3'-HYDROXYLASE

Total number of rows: 18352

Table truncated, full table size 3195 Kbytes.




Table 2: Seed coat development results (Merged seed coat development, single channel approach,4 biological reps merged in GeneSpringGX7.3, full data set (18352) for cultivars OX736 and OX951, Gm-b10BB EST's had 4 replicate spots per array, these results are the average of 32 analyses) header descriptions
Group A, 3398 EST's with significant change over time & average background intensity >10 in any condition; B, 12285 EST's with little change over time (filter set at max 2.0 and min 0.5 on normalized data) & average background intensity >10 in any condition; C, 2669 EST's with average background intensity <10 in all conditions
Systematic name
Genbank
Normalized OX736 Early Early development stage, 10 to 20 days after pollination (DAP), data normalized in GeneSpring, per chip to 50th percentile and per gene to median of the measurements of that gene, average of 8 measurements single spotted EST's*
sVOL OX736 Early Early development stage, 10 to 20 days after pollination (DAP), background subtracted intensity, average of readings from 8 hybridizations*
Normalized OX736 2 Mid Mid development stage, 12 to 35 DAP, data normalized in GeneSpring, per chip to 50th percentile and per gene to median of the measurements of that gene, average of 8 measurements single spotted EST's*
sVOL OX736 Mid
Normalized OX736 3 Late Late development stage, 36 to 50 DAP, data normalized in GeneSpring, per chip to 50th percentile and per gene to median of the measurements of that gene, average of 8 measurements single spotted EST's*
sVOL OX736 Late
Normalized OX951 1 Early Early development stage, 10 to 20 days after pollination (DAP), data normalized in GeneSpring, per chip to 50th percentile and per gene to median of the measurements of that gene, average of 8 measurements single spotted EST's*
sVOL OX951 Early
Normalized OX951 2 Mid Mid development stage, 12 to 35 DAP, data normalized in GeneSpring, per chip to 50th percentile and per gene to median of the measurements of that gene, average of 8 measurements single spotted EST's*
sVOL OX951 Mid
Normalized OX951 3 Late Late development stage, 36 to 50 DAP, data normalized in GeneSpring, per chip to 50th percentile and per gene to median of the measurements of that gene, average of 8 measurements single spotted EST's*
sVOL OX951 Late
Best match BlastX August 2004

Data table
Group Systematic name Genbank Normalized OX736 Early sVOL OX736 Early Normalized OX736 2 Mid sVOL OX736 Mid Normalized OX736 3 Late sVOL OX736 Late Normalized OX951 1 Early sVOL OX951 Early Normalized OX951 2 Mid sVOL OX951 Mid Normalized OX951 3 Late sVOL OX951 Late Best match BlastX August 2004
B Gm-b10BB-1 AW318030 1.06 215 1.22 230 0.93 217 0.84 229 0.98 208 0.79 246 ELONGATION FACTOR 1-ALPHA
B Gm-b10BB-2 BE806777 1.12 42 1.33 47 0.69 30 1.03 49 1.25 49 0.73 44 PHENYLALANINE AMMONIA-LYASE 1
B Gm-b10BB-3 AI855764 0.97 18 1.42 24 1.07 24 0.89 22 1.12 21 1.02 31 CHALCONE SYNTHASE 1
B Gm-b10BB-4 AW707011 0.94 20 1.19 24 0.86 23 0.87 25 0.99 23 0.94 35 CHALCONE SYNTHASE 1
C Gm-b10BB-5 L03352 0.58 5 0.69 6 0.55 6 0.57 6 0.59 6 0.56 9 Glycine max chalcone synthase (chs6) gene, complete cds
B Gm-b10BB-6 AI437793 1.34 25 0.93 21 0.55 13 1.23 28 0.95 23 0.81 25 CHALCONE SYNTHASE 7
A Gm-b10BB-7 AI441937 1.43 31 1.05 25 0.47 13 1.25 32 1.07 28 0.64 22 CHS8 CHALCONE SYNTHASE 8
A Gm-b10BB-9 BG157194 0.74 27 1.53 45 0.91 40 0.72 27 2.35 70 1.08 51 CHALCONE--FLAVONONE ISOMERASE
B Gm-b10BB-10 BG157194 0.66 66 1.08 110 0.99 125 0.57 65 1.94 190 1.17 152 CHALCONE--FLAVONONE ISOMERASE
A Gm-b10BB-11 AI930858 0.73 31 1.49 58 0.97 53 0.68 33 2.53 102 1.13 62 CHALCONE ISOMERASE
A Gm-b10BB-12 AI900038 1.18 122 1.72 169 0.49 55 0.94 107 1.67 163 0.41 60 NARINGENIN,2-OXOGLUTARATE 3-DIOXYGENASE
A Gm-b10BB-13 AW277481 1.37 156 1.5 184 0.41 56 1.07 138 1.29 158 0.34 59 NARINGENIN,2-OXOGLUTARATE 3-DIOXYGENASE
A Gm-b10BB-14 AW156539 1.67 56 1.8 78 0.45 20 1.06 47 1.15 49 0.31 18 FLAVONOL SYNTHASE
A Gm-b10BB-15 BE059354 1.13 12 1.81 17 0.56 7 0.91 10 1.51 14 0.41 8 FLAVONOL SYNTHASE
B Gm-b10BB-17 AW830233 0.64 39 1.12 61 0.94 75 0.6 40 1.87 110 1.09 92 CYTOCHROME P450 71D9
A Gm-b10BB-18 AW569417 0.69 13 1.15 22 0.97 24 0.65 14 2.34 43 1.26 30 CYTOCHROME P450 71D8
C Gm-b10BB-19 BE805102 0.27 2 0.5 5 0.33 5 0.25 3 0.9 9 0.4 6 CYTOCHROME P450 71D8
B Gm-b10BB-20 BG157080 0.87 17 1.35 22 0.98 22 0.84 19 1.44 27 0.87 29 FLAVONOID 3', 5'-HYDROXYLASE LIKE PROTEIN.
C Gm-b10BB-21 BG041082 0.79 6 0.75 6 0.65 8 0.78 8 0.65 6 0.57 10 FLAVONOID 3', 5'-HYDROXYLASE-LIKE PROTEIN.
C Gm-b10BB-22 BF069512 0.42 4 0.5 4 0.35 4 0.4 4 0.49 4 0.34 5 FLAVONOID 3'-HYDROXYLASE

Total number of rows: 18352

Table truncated, full table size 3766 Kbytes.




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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE4276_RAW.tar 3.6 Gb (http)(custom) TAR (of TIFF, TXT)
GSE4276_seed_coat_development_results.txt 3.8 Mb (ftp)(http) TXT
GSE4276_seed_coat_ratio_results.txt 3.2 Mb (ftp)(http) TXT

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