| Data Type | Data Conditions | Literature | Link to Paper | Link to Data |
|---|---|---|---|---|
| Transcriptomics rna-seq |
Root tip
Root Leaves Green Pods Flower Apical Meristem Nodule 12hr inoculated root hair 12hr uninoculated root hair 24hr inoculated root hair 24hr uninoculated root hair 48hr inoculated root hair 48hr uninoculated root hair 48hr Stripped Root |
Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G. An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J. 2010 Jul 1;63(1):86-99. | ||
| Transcriptomics rna-seq |
Nodule
Root Young leaf Flower 1 cm pod Pod shell 10 DAF Pod shell 14 DAF Seed 10 DAF Seed 14 DAF Seed 21 DAF Seed 25 DAF Seed 28 DAF Seed 35 DAF Seed 42 DAF |
Severin AJ, Woody JL, Bolon YT, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, Graham MA, Cannon SB, May GD, Vance CP, Shoemaker RC. RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol. 2010 Aug 5;10:160. | ||
| Transcriptomics microarray (tissue) |
Hypocotyl
Root Pericycle cell Whole seed cotyledon stage Endosperm cotyledon stage Leaf Soybean V2 trifoliate leaf strain 2601R Axillary meristem Shoot apical meristem Mature pollen grain |
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| Transcriptomics microarray (stress) |
Iron_Deficient_50uM_Fe(NO3)3_Leaf
Iron_Sufficient_100uM_Fe(NO3)3_Leaf P.sojae_Infected_Hypocotyl_6h P.sojae_Infected_Hypocotyl_12h P.sojae_Infected_Hypocotyl_24h P.sojae_Infected_Hypocotyl_48h Control_Storage_Protein_Suppression_Cotyledon RNAi_Storage_Protein_Suppression1_Cotyledon RNAi_Storage_Protein_Suppression2_Cotyledon Control_Oleosin_Cotyledon RNAi_Oleosin_Suppression1_Cotyledon RNAi_Oleosin_Suppression2_Cotyledon Control_48h_Water_Leaf Treated_48h_NoDBj_Leaf P.pachyrhizi_Control_0h_Leaf P.pachyrhizi_Resistant_6h_Leaf P.pachyrhizi_Susceptible_6h_Leaf P.pachyrhizi_Resistant_12h_Leaf P.pachyrhizi_Susceptible_12h_Leaf P.pachyrhizi_Resistant_48h_Leaf P.pachyrhizi_Susceptible_48h_Leaf P.pachyrhizi_Control_0h_Leaf P.pachyrhizi_Resistant_6h_Leaf P.pachyrhizi_Susceptible_6h_Leaf P.pachyrhizi_Resistant_12h_Leaf P.pachyrhizi_Susceptible_12h_Leaf P.pachyrhizi_Resistant_24h_Leaf P.pachyrhizi_Susceptible_24h_Leaf P.pachyrhizi_Resistant_48h_Leaf P.pachyrhizi_Susceptible_48h_Leaf P.pachyrhizi_Control_0h_Leaf P.pachyrhizi_Resistant_6h_Leaf P.pachyrhizi_Susceptible_6h_Leaf P.pachyrhizi_Resistant_12h_Leaf P.pachyrhizi_Susceptible_12h_Leaf P.pachyrhizi_Resistant_24h_Leaf P.pachyrhizi_Susceptible_24h_Leaf P.pachyrhizi_Resistant_48h_Leaf P.pachyrhizi_Susceptible_48h_Leaf P.pachyrhizi_Uninoculated_Leaf P.pachyrhizi_Inoculated_Leaf P.pachyrhizi_Uninoculated_Leaf P.pachyrhizi_Inoculated_Leaf Pericycle_Cell_Control_2days Syncytium_Infected_5days Pericycle_Cell_Control_2days Syncytium_Infected_10days Syncytium_Infected_2days Syncytium_Infected_10days Syncytium_Infected_5days Pericycle_Cell_Control_2days Syncytium_Infected_2days Syncytium_Infected_10days SCN_Infected_5daypost-inoculation_Root Control_10daypost-inoculation_Root Control_2daypost-inoculation_Root SCN_Infected_5daypost-inoculation_Root SCN_Infected_2daypost-inoculation_Root Control_5daypost-inoculation_Root SCN_Infected_10daypost-inoculation_Root Control_5daypost-inoculation_Root SCN_Infected_2daypost-inoculation_Root Control_2daypost-inoculation_Root Control_10daypost-inoculation_Root SCN_Infected_5daypost-inoculation_Root |
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| Transcriptomics microarray |
Leaf
Root Root tip 5 hr segment 1 Root tip 5 hr segment 2 Root tip 48 hr segment 1 Root tip 48 hr segment 2 Root tip 48 hr segment 3 |
Nguyen Lab (unpublished) | ||
| Proteomics |
Root control 15 min
Root control 45 min Root control 12hr Root control 48hr Root disease 15 min Root disease 45 min Root disease 12hr Root disease 48hr Root hair control 0 min Root hair control 15 min Root hair control 45 min Root hair control 3 hr Root hair control 12 hr Root hair control 24 hr Root hair control 36 hr Root hair control 48 hr Root hair control 72 hr Root hair disease 0 min Root hair disease 15 min Root hair disease 45 min Root hair disease 3 hr Root hair disease 12 hr Root hair disease 24 hr Root hair disease 36 hr Root hair disease 48 hr Root hair disease 72 hr |
Stacey Lab (unpublished) | ||
| Proteomics |
Seed 2WAF
Seed 3WAF Seed 4WAF Seed 5WAF Seed 6WAF |
Hajduch M, Ganapathy A, Stein JW, Thelen JJ. A systematic proteomic study of seed filling in soybean. Establishment of high-resolution two-dimensional reference maps, expression profiles, and an interactive proteome database. Plant Physiol. 2005 Apr;137(4):1397-419. | ||
| Metabolomics (LCMS, GCMS) |
Root hair inoculated 0 hr
Root hair inoculated 12 hr Root hair inoculated 18 hr Root hair inoculated 24 hr Root hair inoculated 36 hr Root hair inoculated 48 hr Root hair uninoculated 0 hr Root hair uninoculated 12 hr Root hair uninoculated 18 hr Root hair uninoculated 24 hr Root hair uninoculated 36 hr Root hair uninoculated 48 hr Stripped root inoculated 0 hr Stripped root inoculated 12 hr Stripped root inoculated 18 hr Stripped root inoculated 24 hr Stripped root inoculated 36 hr Stripped root inoculated 48 hr Stripped root uninoculated 0 hr Stripped root uninoculated 12 hr Stripped root uninoculated 18 hr Stripped root uninoculated 24 hr Stripped root uninoculated 36 hr Stripped root uninoculated 48 hr |
Brechenmacher L, Lei Z, Libault M, Findley S, Sugawara M, Sadowsky MJ, Sumner LW, Stacey G. Soybean metabolites regulated in root hairs in response to the symbiotic bacterium Bradyrhizobium japonicum. Plant Physiol. 2010 Aug;153(4):1808-22. | ||
| Metabolomics (LCMS, GCMS) |
Root polar
Seed Nonpolar Seed polar Control Water Stressed |
Nguyen Lab (unpublished) | ||
| EST |
Drought root tip 5 hr segment 1
Drought root tip 5 hr segment 2 Drought root tip 48 hr segment 1 Drought root tip 48 hr segment 2 |
Valliyodan,B., Huang,S., Joshi,T., Hernandez,A., Spollen,W.G., Bohnert,H.J., Duke,M.V., Liu,X., Scheffler,B.E., Sharp,R.E., Xu,D., Springer,G.K., Stacey,G., Nguyen,H.T. EST Analysis of Soybean Root Tip Under Drought Stress. 2005. Unpublished. | ||
| 5' RATE |
Root Controlled
Root Stressed |
Nguyen Lab (unpublished) | ||
| Full length cdna |
Drought
Inoculation |
Stacey Lab (unpublished)
Nguyen Lab (unpublished) |
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| miRNA |
Root
Nodule Flower Seed Stripped Root |
Joshi T, Yan Z, Libault M, Jeong DH, Park S, Green PJ, Sherrier DJ, Farmer A, May G, Meyers BC, Xu D, Stacey G. Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S14. | ||
| SNP | Williams vs Forrest (7947) | Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. SNP discovery by high-throughput sequencing in soybean. BMC Genomics. 2010 Aug 11;11:469. | ||
| SNP | Magellan vs PI (2631) | Nguyen Lab (unpublished) | ||
| Gene family | Transcription factors | Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen HT, Xu D, Stacey G, Cheng J. SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol. 2010 Jan 18;10:14. | ||
| Gene family | Cytochrome P450 | Guttikonda SK, Trupti J, Bisht NC, Chen H, An YQ, Pandey S, Xu D, Yu O. Whole genome co-expression analysis of soybean cytochrome P450 genes identifies nodulation-specific P450monooxygenases. BMC Plant Biol. 2010 Nov 9;10:243. |