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Series GSE4194 Query DataSets for GSE4194
Status Public on Jan 01, 2007
Title Soybean cultivars RCAT-Angora & Harovinton, embryo comparison and development
Organism Glycine max
Experiment type Expression profiling by array
Genome variation profiling by array
Genome variation profiling by genome tiling array
Summary Soybean cultivars RCAT-Angora & Harovinton, comparison of embryos at 30,40,50,60 & 70 days after pollination (dap) and seed development within each cultivar"
Keywords: time course
 
Overall design 42 microarray slides GPL3015; 2 soybean cultivars, RCAT-Angora (with high seed isoflavonoid content)& Harovinton (with low seed isoflavonoid content); 2 technical reps for each time point (dye swap); 4 biological reps from 2 locations at London (L) & Delhi (D) Ontario & 2 consecutive growing seasons 2003 and 2004; 5 time points of 30, 40, 50, 60 & 70 dap for D04, L03, L04 and 4 time points of 30, 40, 50 and 70 dap for D03. In addition 2 slides for seed development confirmation D03 30 vs 70 dap RCAT-Angora and 2 for genomic comparison of RCAT-Angora & Harovinton were included. Slide data was analyzed in GeneSpringGX7.3, Agilent technologies, using background subtracted values. The ratio for RCAT/Hvtn was calculated from the 2 colour hybridization (same slide) and the relative expression for embryo development as a function of time (single channel approach) was calculated for each cultivar. The slide identities are L04 GSM94935 - 94944; genomic GSM95945-94946; L03 GSM94947 - 94956; D04 GSM94957 to 94966; D03 GSM94967 - 94976
 
Contributor(s) Dhaubhadel S, Gijzen M, Moy P
Citation(s) 17098860
Submission date Feb 07, 2006
Last update date May 19, 2012
Contact name Sangeeta Dhaubhadel
E-mail(s) [email protected]
Phone 519-457-1470 x670
Fax 519-457-3997
Organization name SCPFRC London
Department Agriculture & Agrifood Canada
Lab Plant Molecular Biology
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 (42)
GSM94935 #150561 Soybean embryo, RCAT-Angora & Harovinton, London 2004 time course
GSM94936 #150562 Soybean embryo, RCAT-Angora & Harovinton, London 2004 time course
GSM94937 #150557 Soybean embryo, RCAT-Angora & Harovinton, London 2004 time course
Relations
BioProject PRJNA95045

Table 1: Cultivar ratio results (Merged normalized data of the ratio, RCAT divided by Harovinton, 4 biological reps merged in GeneSpringGX7.3, full soybean data set (18352), Average raw data intensities are published in the GSE4194 embryo development full data set, Gm-b10BB EST's had 4 replicate spots per array, these results are the average of 32 analyses) header descriptions
Group A1, 733 EST's up regulated, minimum change 1.5x, greater in RCAT than Hvtn in any time point and average sVOL >10 in any condition; A2, 458 EST's down regulated, minimum change 1.5x, greater in Hvtn than RCAT in any time point and average sVOL >10 in any condition; B, 10337 EST's with very little change in ratio (less than 1.5x change) and average background intensity >10 in any condition; C ,6873 EST's with low average sVOL <10 in all times and both cultivars, these are lower than twice the background intensity and not included in the data mining
Systematic Name
Genbank
RCAT/Hvtn 30 DAP
RCAT/Hvtn 40 DAP
RCAT/Hvtn 50 DAP
RCAT/Hvtn 60 DAP
RCAT/Hvtn 70 DAP
Best match BlastX August 2004

Data table
Group Systematic Name Genbank RCAT/Hvtn 30 DAP RCAT/Hvtn 40 DAP RCAT/Hvtn 50 DAP RCAT/Hvtn 60 DAP RCAT/Hvtn 70 DAP Best match BlastX August 2004
B Gm-b10BB-1 AW318030 1.29 1.04 1.1 1.01 0.88 EF1-a : ELONGATION FACTOR 1-ALPHA
B Gm-b10BB-2 BE806777 1.36 1.34 1.1 0.98 1.31 PAL PHENYLALANINE AMMONIA-LYASE 1
B Gm-b10BB-3 AI855764 1.15 0.93 1.17 1.19 0.99 CHS1 :CHALCONE SYNTHASE 1
B Gm-b10BB-4 AW707011 1.08 1.06 1.12 1.15 1.07 CHS1 : Chalcone synthase gene 1
C Gm-b10BB-5 L03352 1.3 1 1.07 1.06 1.07 Glycine max chalcone synthase (chs6) gene, complete cds
A1 Gm-b10BB-6 AI437793 1.16 1.5 1.52 0.98 2.55 CHALCONE SYNTHASE 7
A1 Gm-b10BB-7 AI441937 1.28 1.69 1.63 1.04 2.57 CHS8 CHALCONE SYNTHASE 8
B Gm-b10BB-9 BG157194 1.16 0.97 1.02 1.4 1.18 CI :CHALCONE--FLAVONONE ISOMERASE
B Gm-b10BB-10 BG157194 1.05 1.02 0.97 1.04 1.08 CI : CHALCONE--FLAVONONE ISOMERASE
B Gm-b10BB-11 AI930858 1.17 0.89 1.02 1.22 1.07 CI : CHALCONE ISOMERASE
A1 Gm-b10BB-12 AI900038 1.09 1.01 1.02 1.26 2.12 NARINGENIN,2-OXOGLUTARATE 3-DIOXYGENASE
C Gm-b10BB-13 AW277481 0.74 0.84 0.96 0.88 0.9 NARINGENIN,2-OXOGLUTARATE 3-DIOXYGENASE
B Gm-b10BB-14 AW156539 0.76 0.89 1.05 0.8 0.85 Fols : FLAVONOL SYNTHASE
B Gm-b10BB-15 BE059354 0.81 1.19 0.99 0.89 0.86 Fols : FLAVONOL SYNTHASE
B Gm-b10BB-17 AW830233 1.1 1.01 1 1.18 1.01 F3'5'H :CYTOCHROME P450 71D9
B Gm-b10BB-18 AW569417 1.23 0.94 0.99 1.43 1.1 F3'5'H :CYTOCHROME P450 71D8
A1 Gm-b10BB-19 BE805102 1.15 0.99 0.98 1.53 0.83 CYTOCHROME P450 71D8
B Gm-b10BB-20 BG157080 1.02 0.87 1.04 1.3 0.92 F3'5'H :FLAVONOID 3', 5'-HYDROXYLASE LIKE PROTEIN.
C Gm-b10BB-21 BG041082 1.17 0.99 0.97 0.97 0.82 FLAVONOID 3', 5'-HYDROXYLASE-LIKE PROTEIN.
C Gm-b10BB-22 BF069512 0.75 1.05 1.1 1 0.86 FLAVONOID 3'-HYDROXYLASE

Total number of rows: 18352

Table truncated, full table size 3369 Kbytes.




Table 2: Embryo development results (merged embryo development, single channel approach,4 biological reps merged in GeneSpringGX7.3, full data set (18352) for cultivarsHarovinton (Hvtn) and RCAT - Angora (RCAT), Gm-b10BB EST's had 4 replicate spots per array, these results are the average of 32 analyses) header descriptions
Group A, 5910 EST's with significant change over time & average background subtracted intensity >10 in any condition; B, 5570 EST's with very little change over time & average background subtracted intensity >10 in any condition; C, 6872 EST's with average background intensity <10 in all times and both cultivars, these are less than 2x above background and not included in data mining
Systematic name
Genbank
Normalized Hvtn 30 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 Hvtn 30 DAP background subtracted intensity, average of readings from 8 hybridizations*
Normalized Hvtn 40 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 Hvtn 40 DAP background subtracted intensity, average of readings from 8 hybridizations*
Normalized Hvtn 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 Hvtn 50 DAP background subtracted intensity, average of readings from 8 hybridizations*
Normalized Hvtn 60 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 Hvtn 60 DAP background subtracted intensity, average of readings from 8 hybridizations*
Normalized Hvtn 70 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 Hvtn 70 DAP background subtracted intensity, average of readings from 8 hybridizations*
Normalized RCAT 30 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 RCAT 30 DAP background subtracted intensity, average of readings from 8 hybridizations*
Normalized RCAT 40 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 RCAT 40 DAP background subtracted intensity, average of readings from 8 hybridizations*
Normalized RCAT 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 RCAT 50 DAP background subtracted intensity, average of readings from 8 hybridizations*
Normalized RCAT 60 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 RCAT 60 DAP background subtracted intensity, average of readings from 8 hybridizations*
Normalized RCAT 70 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 RCAT 70 DAP background subtracted intensity, average of readings from 8 hybridizations*
Best match BlastX August 2004

Data table
Group Systematic name Genbank Normalized Hvtn 30 DAP sVOL Hvtn 30 DAP Normalized Hvtn 40 DAP sVOL Hvtn 40 DAP Normalized Hvtn 50 DAP sVOL Hvtn 50 DAP Normalized Hvtn 60 DAP sVOL Hvtn 60 DAP Normalized Hvtn 70 DAP sVOL Hvtn 70 DAP Normalized RCAT 30 DAP sVOL RCAT 30 DAP Normalized RCAT 40 DAP sVOL RCAT 40 DAP Normalized RCAT 50 DAP sVOL RCAT 50 DAP Normalized RCAT 60 DAP sVOL RCAT 60 DAP Normalized RCAT 70 DAP sVOL RCAT 70 DAP Best match BlastX August 2004
B Gm-b10BB-1 AW318030 1.02 167 0.78 128 0.83 163 0.79 135 1.72 160 1.24 171 0.84 156 0.96 186 0.77 144 1.63 149 ELONGATION FACTOR 1-ALPHA
A Gm-b10BB-2 BE806777 0.71 15 0.57 13 1.09 28 1.47 39 1.56 19 0.91 17 0.74 18 1.23 29 1.34 43 2.07 25 PHENYLALANINE AMMONIA-LYASE 1
A Gm-b10BB-3 AI855764 0.71 11 0.53 8 0.61 11 0.64 12 0.89 9 0.84 12 0.47 9 0.72 12 0.72 13 0.87 9 CHALCONE SYNTHASE 1
A Gm-b10BB-4 AW707011 0.7 10 0.46 7 0.61 10 0.52 9 0.83 8 0.75 10 0.45 8 0.68 11 0.59 10 0.81 8 CHALCONE SYNTHASE 1
C Gm-b10BB-5 L03352 0.19 3 0.12 1 0.16 3 0.14 3 0.22 2 0.29 4 0.12 2 0.14 3 0.13 2 0.22 2 Glycine max chalcone synthase (chs6) gene, complete cds
A Gm-b10BB-6 AI437793 0.38 6 0.38 6 0.71 22 2.03 56 6.72 56 0.45 6 0.58 12 1.1 18 1.89 47 17.98 164 CHALCONE SYNTHASE 7
A Gm-b10BB-7 AI441937 0.46 7 0.44 7 0.74 22 2.26 73 6.63 62 0.62 9 0.72 13 1.21 22 2.22 68 18.15 160 CHS8 CHALCONE SYNTHASE 8
A Gm-b10BB-9 BG157194 1.14 127 1.14 125 1.27 173 1.22 140 0.27 20 1.23 117 1.15 141 1.33 182 1.62 201 0.33 24 CHALCONE--FLAVONONE ISOMERASE
A Gm-b10BB-10 BG157194 1.51 379 1.38 348 1.26 392 1.37 380 0.29 58 1.6 357 1.35 378 1.26 408 1.34 406 0.33 58 CHALCONE--FLAVONONE ISOMERASE
A Gm-b10BB-11 AI930858 1.34 246 1.27 239 1.34 292 1.25 250 0.19 25 1.52 251 1.16 237 1.39 306 1.48 307 0.21 29 CHALCONE ISOMERASE
B Gm-b10BB-12 AI900038 1.12 58 0.98 50 1.22 77 1.12 71 0.67 23 1.09 46 1.01 57 1.28 77 1.35 82 1.46 47 NARINGENIN,2-OXOGLUTARATE 3-DIOXYGENASE
C Gm-b10BB-13 AW277481 0.12 2 0.1 1 0.11 2 0.15 2 0.22 2 0.12 1 0.09 1 0.1 2 0.12 2 0.2 2 NARINGENIN,2-OXOGLUTARATE 3-DIOXYGENASE
A Gm-b10BB-14 AW156539 0.35 8 0.45 7 0.4 16 0.37 13 0.3 3 0.27 4 0.41 9 0.38 11 0.31 7 0.24 2 FLAVONOL SYNTHASE
A Gm-b10BB-15 BE059354 0.28 5 0.41 6 0.38 10 0.4 12 0.36 3 0.27 3 0.51 8 0.34 8 0.34 7 0.3 3 FLAVONOL SYNTHASE
A Gm-b10BB-17 AW830233 1.18 260 1.35 263 1.24 290 1.4 296 0.4 50 1.27 227 1.37 294 1.26 307 1.58 354 0.41 52 CYTOCHROME P450 71D9
A Gm-b10BB-18 AW569417 1.2 126 1.26 130 1.53 177 1.2 121 0.11 9 1.38 122 1.25 140 1.54 186 1.65 185 0.12 8 CYTOCHROME P450 71D8
A Gm-b10BB-19 BE805102 1.1 17 1.09 15 1.55 24 1.21 17 0.22 2 1.2 15 1.08 17 1.56 26 1.75 28 0.18 1 CYTOCHROME P450 71D8
A Gm-b10BB-20 BG157080 0.52 8 0.73 9 0.77 13 0.75 11 0.26 2 0.53 6 0.64 9 0.83 13 0.95 15 0.24 2 FLAVONOID 3', 5'-HYDROXYLASE LIKE PROTEIN.
C Gm-b10BB-21 BG041082 0.2 4 0.15 2 0.17 3 0.09 1 0.26 4 0.26 4 0.15 3 0.17 3 0.09 1 0.22 3 FLAVONOID 3', 5'-HYDROXYLASE-LIKE PROTEIN.
C Gm-b10BB-22 BF069512 0.12 1 0.13 2 0.11 2 0.09 1 0.15 1 0.12 1 0.14 3 0.13 2 0.09 1 0.16 1 FLAVONOID 3'-HYDROXYLASE

Total number of rows: 18352

Table truncated, full table size 4261 Kbytes.




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Supplementary file Size Download File type/resource
GSE4194_RAW.tar 6.3 Gb (http)(custom) TAR (of TIFF, TXT)
GSE4194_cultivar_ratio_results.txt 3.3 Mb (ftp)(http) TXT
GSE4194_embryo_development_results.txt 4.3 Mb (ftp)(http) TXT

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