| Data Type | Sample Name | Data Conditions | Literature | Link to Paper | Link to Data | Data Version |
|---|---|---|---|---|---|---|
| Germplasm PI Data | USDA Agricultural Research Service (ARS) | Version 1.0 | ||||
| CDNA Data (Dataset1-Dataset11) |
AC_12h_v_0h_log2ratio
AC_24h_v_0h_log2ratio AC_36h_v_0h_log2ratio AC_24h_v_12h_log2ratio AC_36h_v_12h_log2ratio AC_36h_v_24h_log2ratio 24C_log2ratio 4C_log2ratio 1C_log2ratio 24T_log2ratio 4T_log2ratio 1T_log2ratio CvT_log2ratio HRT2vsMgCl2T2_log2Ratio VIRT2vsMgCl2T2_log2Ratio HRT2vsVIRT2_log2Ratio HRT8vsMgCl2T8_log2Ratio VIRT8vsMgCl2T8_log2Ratio HRT8vsVIRT8_log2Ratio HRT24vsMgCl2T24_log2Ratio VIRT24vsMgCl2T24_log2Ratio HRT24vsVIRT24_log2Ratio VIRT8vsVIRT2_log2Ratio VIRT24vsVIRT8_log2Ratio HRT8vsHRT2_log2Ratio HRT24vsHRT8_log2Ratio MgCl2T2vsT0_log2Ratio NOD1T0_LOG2RATIO NOD1T01_LOG2RATIO NOD1T03_LOG2RATIO NOD1T06_LOG2RATIO NOD1T12_LOG2RATIO NOD1T24_LOG2RATIO NOD1T48_LOG2RATIO NOD1T72_LOG2RATIO OxO_12h_v_0h OxO_24h_v_0h OxO_36h_v_0h OxO_24h_v_12h OxO_36h_v_12h OxO_36h_v_24h RTGTHT4T0_LOG2RATIO RTGTHT8T0_LOG2RATIO RTGTHT8T4_LOG2RATIO RTGTHT16T0_LOG2RATIO RTGTHT16T8_LOG2RATIO PI_vs_EX_inoc_log2Ratio PI_vs_W82_inoc_log2Ratio W82_vs_EX_inoc_log2Ratio PIinoc_vs_PImock_log2Ratio W82inoc_vs_W82mock_log2Ratio EXinoc_vs_EXmock_log2Ratio PI_vs_W82_mocks_log2Ratio W82_vs_EX_mocks_log2Ratio PI_vs_EX_mocks_log2Ratio NOD2T4DPI_LOG2RATIO NOD2T8DPI_LOG2RATIO NOD2T16DPI_LOG2RATIO AW_T1_LOG2RATIO AW_T2_LOG2RATIO AW_T4_LOG2RATIO AW_T8_LOG2RATIO BW_T1_LOG2RATIO BW_T2_LOG2RATIO BW_T4_LOG2RATIO BW_T8_LOG2RATIO AB_T1_LOG2RATIO AB_T2_LOG2RATIO AB_T4_LOG2RATIO AB_T8_LOG2RATIO T12T0_AC_LOG2RATIO T12T0_OXO_LOG2RATIO T24T12_AC_LOG2RATIO T24T12_OXO_LOG2RATIO T24T0_AC_LOG2RATIO T24T0_OXO_LOG2RATIO OXOAC_T0_LOG2RATIO OXOAC_T12_LOG2RATIO OXOAC_T24_LOG2RATIO T14VST8_W_LOG2RATIO T14VST8_PI_LOG2RATIO PIVSW_T8_LOG2RATIO PIVSW_T14_LOG2RATIO PIVSW_T0_LOG2RATIO |
1. Zhu J, Patzoldt WL, Shealy RT, Vodkin LO, Clough SJ, Tranel PJ. Transcriptome response to glyphosate in sensitive and resistant soybean. J Agric Food Chem. 2008 Aug 13;56(15):6355-63. Epub 2008 Jul 18.
2. Zou J, Rodriguez-Zas S, Aldea M, Li M, Zhu J, Gonzalez DO, Vodkin LO, DeLucia E, Clough SJ.Expression profiling soybean response to Pseudomonas syringae reveals new defense-related genes and rapid HR-specific downregulation of photosynthesis.Mol Plant Microbe Interact. 2005 Nov;18(11):1161-74. 3. Brechenmacher L, Kim MY, Benitez M, Li M, Joshi T, Calla B, Lee MP, Libault M, Vodkin LO, Xu D, Lee SH, Clough SJ, Stacey G.Transcription profiling of soybean nodulation by Bradyrhizobium japonicum.Mol Plant Microbe Interact. 2008 May;21(5):631-45. 4. Zhu, J., Patzoldt, W.L., Radwan, O., Tranel, P.J., Clough, S.J. 2009. Effects of Photosystem II Interfering Herbicides Atrazine and Bentazon on the Soybean Transcriptome. The Plant Genome. 2:191-205. 5. Calla, B., Vuong, T., Radwan, O., Hartman, G.L., Clough, S.J. 2009. Gene Expression Profiling Soybean Stem Tissue Early Response to Sclerotinia sclerotiorum and in Silico Mapping in Relation to Resistance Markers. The Plant Genome. 2:149-166. |
Version 1.0 | |||
| Oligo Data (Dataset1-Dataset4) |
rpg1_AvrB_v_Mock_2h
rpg1_AvrB_v_Mock_4h rpg1_AvrB_v_Mock_8h rpg1_NoAvrB_v_Mock_2h rpg1_NoAvrB_v_Mock_4h rpg1_NoAvrB_v_Mock_8h rpg1_AvrB_v_NoAvrB_2h rpg1_AvrB_v_NoAvrB_4h rpg1_AvrB_v_NoAvrB_8h rpg1_NoAvrB_4h_v_2h rpg1_NoAvrB_8h_v_4h rpg1_NoAvrB_8h_v_2h rpg1_AvrB_4h_v_2h rpg1_AvrB_8h_v_4h rpg1_AvrB_8h_v_2h rpg1_Mock_4h_v_2h rpg1_Mock_8h_v_4h rpg1_Mock_8h_v_2h OxOvAC_H20_24_log2ratio OxOvAC_H20_55_log2ratio OxOvAC_OA_55_log2ratio H2O24vH2O55_AC_log2ratio H2O24vH2O55_OxO_log2ratio H2O24vH2O55_log2ratio OA24vH2O24_AC_log2ratio OA24vH2O24_OxO_log2ratio OA24vH2O24_log2ratio OA24vH2O55_AC_log2ratio OA24vH2O55_OxO_log2ratio OA24vH2O55_log2ratio RPG1_AvrB_v_Mock_2h RPG1_AvrB_v_Mock_4h RPG1_AvrB_v_Mock_8h RPG1_NoAvrB_v_Mock_2h RPG1_NoAvrB_v_Mock_4h RPG1_NoAvrB_v_Mock_8h RPG1_AvrB_v_NoAvrB_2h RPG1_AvrB_v_NoAvrB_4h RPG1_AvrB_v_NoAvrB_8h RPG1_NoAvrB_4h_v_2h RPG1_NoAvrB_8h_v_2h RPG1_NoAvrB_8h_v_4h T8vT4vir_log2ratio T8vT4avr_log2ratio T8vT4mock_log2ratio T4vT2vir_log2ratio T4vT2avr_log2ratio T4vT2mock_log2ratio T8vT2vir_log2ratio T8vT2avr_log2ratio T8vT2mock_log2ratio AvrvVir2_log2ratio AvrvVir4_log2ratio AvrvVir8_log2ratio AvrvMock2_log2ratio AvrvMock4_log2ratio AvrvMock8_log2ratio VirvMock2_log2ratio VirvMock4_log2ratio VirvMock8_log2ratio |
Clough Lab (unpublished) | Version 1.0 | |||
| Epigenomics Methylation Data | 4 genotypes PAMP Treatment |
11268_CG/C
11268_CHG/C 11268_CHH/C 11272_CG/C 11272_CHG/C 11272_CHH/C LD_CG/C LD_CHG/C LD_CHH/C LDX_CG/C LDX_CHG/C LDX_CHH/C |
Schmitz, R.J., He, Y., Valdes-Lopez, O., Khan, S.M., Joshi, T., Urich, M.A., Nery, J.R., Diers, B., Xu, D., Stacey, G., et al. (2013). Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res. 23, 1663-1674. | Version 1.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->1) |
Tissues & Seed time points |
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. | Version 1.0 | ||
| Transcriptomics RPKM RNA-seq (Datase->2) |
Tissues & B. jap Inoculation time points |
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. | Version 1.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->3) |
Chitotetraose & Flg22 Control and Treatment; Control (H), Chitotetraose (C), Flg22 (F) and Flg22-Chitotetraose (FC) |
H1: Mock (1st replication)
C2: Chitotetraose (1st replication) F3: Flg22 (1st replication) FC4: Flg22 + Chitotetraose (1st replication) H5: Mock (2nd replication) C6: Chitotetraose (2nd replication) F7: Flg22 (2nd replication) FC8: Flg22 + Chitotetraose (2nd replication) |
Stacey Lab (unpublished) | Version 1.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->4) |
4 genotypes Control (C) & PAMP Treatment (P) |
11268_C1
11268_C2 11268_C3 11268_P1 11268_P2 11268_P3 11272_C1 11272_C2 11272_C3 11272_P1 11272_P2 11272_P3 LD_C1 LD_C2 LD_C3 LD_P1 LD_P2 LD_P3 LDX_C1 LDX_C2 LDX_C3 LDX_P1 LDX_P2 LDX_P3 |
Oswaldo Valdes-Lopez, Saad M Khan, Robert J. Schmitz, Shiqi Cui, Jing Qiu, Trupti Joshi, Dong Xu, Brian Diers, Joseph R. Ecker, and Gary Stacey (2014) Genotypic variation of gene expression during the soybean innate immunity response. Plant Genetic Resources. (in press) | Version 1.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->5) |
Aphids infestation effect timepoints on Susceptible (W) & Resistant (BC) lines |
W0rep1
W0rep2 BC0rep1 BC0rep2 W4rep1 W4rep2 BC4rep1 BC4rep2 W8rep1 W8rep2 BC8rep1 BC8rep2 W24rep1 W24rep2 BC24rep1 BC24rep2 W48rep1 W48rep2 BC48rep1 BC48rep2 |
Stacey Lab (unpublished) | Version 1.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->6) |
Root Hair Heat Stress time points |
RH_Rep1_0h_25C
RH_Rep2_0h_25C RH_Rep1_0h_40C RH_Rep2_0h_40C RH_Rep1_3h_25C RH_Rep2_3h_25C RH_Rep1_3h_40C RH_Rep2_3h_40C RH_Rep1_6h_25C RH_Rep2_6h_25C RH_Rep1_6h_40C RH_Rep2_6h_40C RH_Rep1_12h_25C RH_Rep2_12h_25C RH_Rep1_12h_40C RH_Rep2_12h_40C RH_Rep1_24h_25C RH_Rep2_24h_25C RH_Rep1_24h_40C RH_Rep2_24h_40C |
Stacey Lab (unpublished) | Version 1.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->7) |
Stripped root Heat Stress time points |
STR_RT_Rep1_0h_25C
STR_RT_Rep2_0h_25C STR_RT_Rep1_0h_40C STR_RT_Rep2_0h_40C STR_RT_Rep1_3h_25C STR_RT_Rep2_3h_25C STR_RT_Rep1_3h_40C STR_RT_Rep2_3h_40C STR_RT_Rep1_6h_25C STR_RT_Rep2_6h_25C STR_RT_Rep1_6h_40C STR_RT_Rep2_6h_40C STR_RT_Rep1_12h_25C STR_RT_Rep2_12h_25C STR_RT_Rep1_12h_40C STR_RT_Rep2_12h_40C STR_RT_Rep1_24h_25C STR_RT_Rep2_24h_25C STR_RT_Rep1_24h_40C STR_RT_Rep2_24h_40C |
Stacey Lab (unpublished) | Version 1.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->8) |
Sclerotinia sclerotiorum mycelia and stem tissue; AC-Colibri cultivar and OxO-transgenic line infiltrated with oxalic acid leaf tissue |
s_3_ACOA
s_3_OXOOA s_4_ACH2O s_4_OXOH2O s_5_MYCELIA_REP1 s_5_STEMS_CTRL s_6_MYCELIA_REP2 S_6_STEMS_INOC |
Clough Lab (unpublished) | Version 1.0 | ||
| Transcriptomics RPKM RNA-seq(Trinity)(Dataset->9) |
Stink bugs CD215 susceptible and mock |
CD215_suseptible_mock1
CD215_suseptible_mock2 CD215_suseptible_mock3 CD215_suseptible_mock4 CD215_suseptible_insect1 CD215_suseptible_insect2 CD215_suseptible_insect3 CD215_suseptible_insect4 |
Clough Lab (unpublished) | Version 1.0 | ||
| Transcriptomics RPKM RNA-seq(Trinity) (Dataset->10) |
Stink bugs IAC100 resistant and mock |
IAC100_resistant_mock1
IAC100_resistant_mock2 IAC100_resistant_mock3 IAC100_resistant_mock4 IAC100_resistant_insect1 IAC100_resistant_insect2 IAC100_resistant_insect3 IAC100_resistant_insect4 |
Clough Lab (unpublished) | Version 1.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->11) |
Root Nutrient Treatments |
Root_NH4
Root_NO3 Root_Sym_cond Root_Urea |
Stacey Lab (unpublished) | Version Wm82.a2.v1 | ||
| Transcriptomics RPKM RNA-seq (Dataset->12) |
Leaf Nutrient Treatments |
Leaf_NH4
Leaf_NO3 Leaf_Sym_cond Leaf_Urea |
Stacey Lab (unpublished) | Version Wm82.a2.v1 | ||
| Transcriptomics RPKM RNA-seq (Dataset->13) |
Drought Flooding Genotype |
P***_Drought_Susceptible_control
P***_Drought_Susceptible_drought PI5*****_Drought_Tolerant_control PI5*****_Drought_Tolerant_drought PI4******_Flooding_Tolerant_control PI4******_Flooding_Tolerant_flooding S**_****_Flooding_Susceptible_control S**_****_Flooding_Susceptible_flooding |
Nguyen Lab (unpublished) | Version 9.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->14) |
Drought Flooding Genotype - Alt. Splicing |
PI5*****_Drought_Tolerant_control
PI5*****_Drought_Tolerant_drought PI4*******_Flooding_Tolerant_control PI4*******_Flooding_Tolerant_flooding |
Nguyen Lab (unpublished) | Version 9.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->15) |
Soybean Root Hormones |
Monk_0.5h_Ctrl1_R1
Monk_0.5h_Ctrl1_R2 Monk_0.5h_Ctrl1_R3 Monk_3h_Ctrl1_R1 Monk_3h_Ctrl1_R2 Monk_3h_Ctrl1_R3 ABA_0.5h_R1 ABA_0.5h_R2 ABA_0.5h_R3 ABA_3h_R1 ABA_3h_R2 ABA_3h_R3 IAA_0.5h_R1 IAA_0.5h_R2 IAA_0.5h_R3 IAA_3h_R1 IAA_3h_R2 IAA_3h_R3 CK_0.5h_R1 CK_0.5h_R2 CK_0.5h_R3 CK_3h_R1 CK_3h_R2 CK_3h_R3 GA_0.5h_R1 GA_0.5h_R2 GA_0.5h_R3 GA_3h_R1 GA_3h_R2 GA_3h_R3 Monk_0.5h_Ctrl2_R1 Monk_0.5h_Ctrl2_R2 Monk_0.5h_Ctrl2_R3 Monk_3h_Ctrl2_R1 Monk_3h_Ctrl2_R2 Monk_3h_Ctrl2_R3 JA_0.5h_R1 JA_0.5h_R2 JA_0.5h_R3 JA_3h_R1 JA_3h_R2 JA_3h_R3 ACC_0.5h_R1 ACC_0.5h_R2 ACC_0.5h_R3 ACC_3h_R1 ACC_3h_R2 ACC_3h_R3 SA_0.5h_R1 SA_0.5h_R2 SA_0.5h_R3 SA_3h_R1 SA_3h_R2 SA_3h_R3 BR_0.5h_R1 BR_0.5h_R2 BR_0.5h_R3 BR_3h_R1 BR_3h_R2 BR_3h_R3 |
Nguyen Lab (unpublished) | Version 9.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->16) |
Soybean Root Over Expression or RNAi Silencing |
Empty_Vector_R1
Empty_Vector_R2 Empty_Vector_R3 GmPRE2_OX_R1 GmPRE2_OX_R2 GmPRE2_OX_R3 GmERF3_OX_R1 GmERF3_OX_R2 GmERF3_OX_R3 GmbZIP1_OX_R1 GmbZIP1_OX_R2 GmbZIP1_OX_R3 Pre_RNAi_R1 Pre_RNAi_R2 |
Nguyen Lab (unpublished) | Version 9.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->17) |
Drought Stress Level and Tissue |
VMS_Root_CK_R1 VMS_Root_CK_R2 VMS_Root_CK_R3 VMS_Root_Stress_R1 VMS_Root_Stress_R2 VMS_Root_Stress_R3 VMS_Stem_CK_R1 VMS_Stem_CK_R2 VMS_Stem_CK_R3 VMS_Stem_Stress_R1 VMS_Stem_Stress_R2 VMS_Stem_Stress_R3 VMS_Leaf_CK_R1 VMS_Leaf_CK_R2 VMS_Leaf_CK_R3 VMS_Leaf_Stress_R1 VMS_Leaf_Stress_R2 VMS_Leaf_Stress_R3 MS_Root_CK_R1 MS_Root_CK_R2 MS_Root_CK_R3 MS_Root_Stress_R1 MS_Root_Stress_R2 MS_Root_Stress_R3 MS_Stem_CK_R1 MS_Stem_CK_R2 MS_Stem_CK_R3 MS_Stem_Stress_R1 MS_Stem_Stress_R2 MS_Stem_Stress_R3 MS_Leaf_CK_R1 MS_Leaf_CK_R2 MS_Leaf_CK_R3 MS_Leaf_Stress_R1 MS_Leaf_Stress_R2 MS_Leaf_Stress_R3 SS_Root_CK_R1 SS_Root_CK_R2 SS_Root_CK_R3 SS_Root_Stress_R1 SS_Root_Stress_R2 SS_Root_Stress_R3 SS_Stem_CK_R1 SS_Stem_CK_R2 SS_Stem_CK_R3 SS_Stem_Stress_R1 SS_Stem_Stress_R2 SS_Stem_Stress_R3 SS_Leaf_CK_R1 SS_Leaf_CK_R2 SS_Leaf_CK_R3 SS_Leaf_Stress_R1 SS_Leaf_Stress_R2 SS_Leaf_Stress_R3 SR_Root_CK_R1 SR_Root_CK_R2 SR_Root_CK_R3 SR_Root_Stress_R1 SR_Root_Stress_R2 SR_Root_Stress_R3 SR_Stem_CK_R1 SR_Stem_CK_R2 SR_Stem_CK_R3 SR_Stem_Stress_R1 SR_Stem_Stress_R2 SR_Stem_Stress_R3 SR_Leaf_CK_R1 SR_Leaf_CK_R2 SR_Leaf_CK_R3 SR_Leaf_Stress_R1 SR_Leaf_Stress_R2 SR_Leaf_Stress_R3 |
Nguyen Lab (unpublished) | Version 9.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->18) |
Seed Germination Stages - Genotype - Location |
PI587982A CSPS mature (PCm)
PI587982A CSPS imbibed (PCi) PI587982A CSPS germinated (PCg) PI587982A ESPS mature (PEm) PI587982A ESPS imbibed (PEi) PI587982A ESPS germinated (PEg) S99-11986 CSPS mature (SCm) S99-11986 CSPS imbibed (SCi) S99-11986 CSPS germinated (SCg) S99-11986 ESPS mature (SEm) S99-11986 ESPS imbibed (SEi) S99-11986 ESPS germinated (SEg) |
Jason Lab (unpublished) | Version 9.0 | ||
| Transcriptomics RPKM RNA-seq (Dataset->19) |
Leaf |
Control vs Drought
Control vs Heat Control vs Heat&Drought |
Sinha R, Shostak B, Induri SP, Sen S, Zandalinas SI, Joshi T, Fritschi FB, Mittler R. Differential transpiration between pods and leaves during stress combination in soybean. Plant Physiol. 2023 Feb 22:kiad114. doi: 10.1093/plphys/kiad114. Epub ahead of print. PMID: 36810691. | Version 2.1 | ||
| Transcriptomics RPKM RNA-seq (Dataset->20) |
Flower |
Control vs Drought
Control vs Heat Control vs Heat&Drought |
Sinha R, Zandalinas SI, Fichman Y, Sen S, Zeng S, Gómez-Cadenas A, Joshi T, Fritschi FB, Mittler R. Differential regulation of flower transpiration during abiotic stress in annual plants. New Phytol. 2022 Jul;235(2):611-629. doi: 10.1111/nph.18162. Epub 2022 May 12. PMID: 35441705; PMCID: PMC9323482. | Version 2.1 | ||
| Transcriptomics RPKM RNA-seq (Dataset->21) |
Anther |
Control vs Drought
Control vs Heat Control vs Heat&Drought |
Sinha R, Induri SP, Peláez-Vico MÁ, Tukuli A, Shostak B, Zandalinas SI, Joshi T, Fritschi FB, Mittler R. The transcriptome of soybean reproductive tissues subjected to water deficit, heat stress, and a combination of water deficit and heat stress. Plant J. 2023 Apr 3. doi: 10.1111/tpj.16222. Epub ahead of print. PMID: 37006191. | Version 2.1 | ||
| Transcriptomics RPKM RNA-seq (Dataset->22) |
Sepal |
Control vs Drought
Control vs Heat Control vs Heat&Drought |
Sinha R, Induri SP, Peláez-Vico MÁ, Tukuli A, Shostak B, Zandalinas SI, Joshi T, Fritschi FB, Mittler R. The transcriptome of soybean reproductive tissues subjected to water deficit, heat stress, and a combination of water deficit and heat stress. Plant J. 2023 Apr 3. doi: 10.1111/tpj.16222. Epub ahead of print. PMID: 37006191. | Version 2.1 | ||
| Transcriptomics RPKM RNA-seq (Dataset->23) |
Stigma |
Control vs Drought
Control vs Heat Control vs Heat&Drought |
Sinha R, Induri SP, Peláez-Vico MÁ, Tukuli A, Shostak B, Zandalinas SI, Joshi T, Fritschi FB, Mittler R. The transcriptome of soybean reproductive tissues subjected to water deficit, heat stress, and a combination of water deficit and heat stress. Plant J. 2023 Apr 3. doi: 10.1111/tpj.16222. Epub ahead of print. PMID: 37006191. | Version 2.1 | ||
| Transcriptomics RPKM RNA-seq (Dataset->24) |
Pod |
Control vs Drought
Control vs Heat Control vs Heat&Drought |
Sinha R, Shostak B, Induri SP, Sen S, Zandalinas SI, Joshi T, Fritschi FB, Mittler R. Differential transpiration between pods and leaves during stress combination in soybean. Plant Physiol. 2023 Feb 22:kiad114. doi: 10.1093/plphys/kiad114. Epub ahead of print. PMID: 36810691. | Version 2.1 | ||
| Transcriptomics RPKM RNA-seq (Dataset->25) |
Ovary |
Control vs Drought
Control vs Heat Control vs Heat&Drought |
Sinha R, Induri SP, Peláez-Vico MÁ, Tukuli A, Shostak B, Zandalinas SI, Joshi T, Fritschi FB, Mittler R. The transcriptome of soybean reproductive tissues subjected to water deficit, heat stress, and a combination of water deficit and heat stress. Plant J. 2023 Apr 3. doi: 10.1111/tpj.16222. Epub ahead of print. PMID: 37006191. | Version 2.1 | ||
| Transcriptomics ReadCount RNA-seq (Dataset->1) |
ATP_ReadCount |
RH_MES_ATP_R1
RH_MES_ATP_R2 RH_Stress_ATP_R1 RH_Stress_ATP_R2 RH_Mock_NF_R1 RH_Mock_NF_R2 RH_Stress_NF_R1 RH_Stress_NF_R2 SRH_MES_ATP_R1 SRH_MES_ATP_R2 SRH_Stress_ATP_R1 SRH_Stress_ATP_R2 SRH_Mock_NF_R1 SRH_Mock_NF_R2 SRH_Stress_NF_R1 SRH_Stress_NF_R2 |
Stacey Lab (unpublished) | Version 9.0 | ||
| Transcriptomics ReadCount RNA-seq (Dataset->2) |
Drought_ReadCount |
RH_00hr_control_R1
RH_00hr_control_R2 RH_00hr_drought_R1 RH_00hr_drought_R2 SR_00hr_control_R1 SR_00hr_control_R2 SR_00hr_drought_R1 SR_00hr_drought_R2 RH_6hr_control_R1 RH_6hr_control_R2 RH_6hr_drought_R1 RH_6hr_drought_R2 SR_6hr_control_R1 SR_6hr_control_R2 SR_6hr_drought_R1 SR_6hr_drought_R2 RH_24hr_control_R1 RH_24hr_control_R2 RH_24hr_drought_R1 RH_24hr_drought_R2 SR_24hr_control_R1 SR_24hr_control_R2 SR_24hr_drought_R1 SR_24hr_drought_R2 |
Stacey Lab (unpublished) | Version 9.0 | ||
| Transcriptomics ReadCount RNA-seq (Dataset->3) |
Nod_factor_ReadCount |
RH_00hr_Mock_R1
RH_00hr_Mock_R2 RH_00hr_NOD_R1 RH_00hr_NOD_R2 SR_00hr_Mock_R1 SR_00hr_Mock_R2 SR_00hr_NOD_R1 SR_00hr_NOD_R2 RH_03hr_Mock_R1 RH_03hr_Mock_R2 RH_03hr_NOD_R1 RH_03hr_NOD_R2 SR_03hr_Mock_R1 SR_03hr_Mock_R2 SR_03hr_NOD_R1 SR_03hr_NOD_R2 RH_12hr_Mock_R1 RH_12hr_Mock_R2 RH_12hr_NOD_R1 RH_12hr_NOD_R2 SR_12hr_Mock_R1 SR_12hr_Mock_R2 SR_12hr_NOD_R1 SR_12hr_NOD_R2 |
Stacey Lab (unpublished) | Version 9.0 | ||
| Transcriptomics ReadCount RNA-seq (Dataset->4) |
Raw_ReadCount |
Co0hrR1 Co0hrR2 Co0hrR3 De1hrR1 De1hrR2 De1hrR3 De6hrR1 De6hrR2 De6hrR3 De12hrR1 De12hrR2 De12hrR3 Na1hrR1 Na1hrR2 Na1hrR3 Na6hrR1 Na6hrR2 Na6hrR3 Na12hrR1 Na12hrR2 Na12hrR3 |
Version 1.0 | |||
| Transcriptomics ReadCount RNA-seq (Dataset->5) |
DESeq_Normalized_ReadCount |
Co0hrR1 Co0hrR2 Co0hrR3 De1hrR1 De1hrR2 De1hrR3 De6hrR1 De6hrR2 De6hrR3 De12hrR1 De12hrR2 De12hrR3 Na1hrR1 Na1hrR2 Na1hrR3 Na6hrR1 Na6hrR2 Na6hrR3 Na12hrR1 Na12hrR2 Na12hrR3 |
Version 1.0 | |||
| Transcriptomics microarray (Dataset -> 1) | AffymetrixLeafRoot & AffymetrixRootSeedlingTip |
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) | Version 1.0 | ||
| Transcriptomics microarray (tissue) (Dataset -> 2) | OrganGeneExpression-Tissue condition |
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 |
|
Version 1.0 | ||
| Transcriptomics microarray (stress) (Dataset -> 3) | Stressgeneexpression-Stress condition |
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 |
|
Version 1.0 | ||
| Transcriptomics microarray (Dataset -> 4) | Affy_HairyRoot_v_NormalRoot | HvN_log2ratio | Version 1.0 | |||
| Transcriptomics microarray (Dataset -> 5) | Affy_Rhizobium_T3SS_mutant |
t3ss_vs_H2O_6h
t3ss_vs_H2O_12h t3ss_vs_H2O_18h |
1. Libault M, Farmer A, Brechenmacher L, Drnevich J, Langley RJ, Bilgin DD, Radwan O, Neece DJ, Clough SJ, May GD, Stacey G. Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection.Plant Physiol. 2010 Feb;152(2):541-52. Epub 2009 Nov 20.
|
Version 1.0 | ||
| Transcriptomics microarray (Dataset -> 6) | Affy_SDS_Leaves |
S5_inf_v_mock_log2ratio
S7_inf_v_mock_log2ratio R5_inf_v_mock_log2ratio R7_inf_v_mock_log2ratio RvS_mock_5_log2ratio RvS_mock_7_log2ratio |
Version 1.0 | |||
| Transcriptomics microarray (Dataset -> 7) | Affy_SDS_Roots |
R_Infect_v_Mock_5d_log2Ratio
R_Infect_v_Mock_7d_log2Ratio S_Infect_v_Mock_5d_log2Ratio S_Infect_v_Mock_7d_log2Ratio R_Infect_v_S_Infect_5d_log2Ratio R_Infect_v_S_Infect_7d_log2Ratio R_mock_v_S_mock_5d_log2Ratio R_mock_v_S_mock_7d_log2Ratio |
1. Radwan O, Liu Y, Clough SJ. Transcriptional analysis of soybean root response to Fusarium virguliforme, the causal agent of sudden death syndrome.Mol Plant Microbe Interact. 2011 Aug;24(8):958-72. | Version 1.0 | ||
| Transcriptomics microarray (Dataset -> 8) | Soybean Cyst Nematode(Heterodera Glycines) |
2007a_FC_2dpi_to_5dpi 2007a_FC_5dpi_to_10dpi 2007a_FC_2dpi_to_10dpi 2007b_FC_PC_to_2dpi 2007b_FC_2dpi_to_5dpi 2007b_FC_5dpi_to_10dpi 2007b_FC_2dpi_to_10dpi 2011_Fold_change |
1. Ithal N, Recknor J, Nettleton D, Hearne L, Maier T, Baum TJ, Mitchum MG.Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean.Mol Plant Microbe Interact. 2007 Mar;20(3):293-305.
2. Ithal N, Recknor J, Nettleton D, Maier T, Baum TJ, Mitchum MG.Developmental transcript profiling of cyst nematode feeding cells in soybean roots.Mol Plant Microbe Interact. 2007 May;20(5):510-25. 3. Kandoth PK, Ithal N, Recknor J, Maier T, Nettleton D, Baum TJ, Mitchum MG.The Soybean Rhg1 locus for resistance to the soybean cyst nematode Heterodera glycines regulates the expression of a large number of stress- and defense-related genes in degenerating feeding cells.Plant Physiol. 2011 Apr;155(4):1960-75. doi: 10.1104/pp.110.167536. Epub 2011 Feb 18. |
Version 1.0 | ||
| Proteomics (Dataset->1) | Root& Roothair control& inoculated Time Points |
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) | Version 1.0 | ||
| Proteomics (Dataset->2) | Seed -> weeks after flowering |
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. | Version 1.0 | ||
| Proteomics (Dataset->3) | Stripped Root and Root Hair Heat Stress Time Points |
Root Hair Time0 25C
Root Hair Time0 40C Root Hair Time3 25C Root Hair Time3 40C Root Hair Time6 25C Root Hair Time6 40C Root Hair Time12 25C Root Hair Time12 40C Root Hair Time24 25C Root Hair Time24 40C Stripped Root Time0 25C Stripped Root Time0 40C Stripped Root Time3 25C Stripped Root Time3 40C Stripped Root Time6 25C Stripped Root Time6 40C Stripped Root Time12 25C Stripped Root Time12 40C Stripped Root Time24 25C Stripped Root Time24 40C |
Stacey Lab (unpublished) | Version 1.0 | ||
| 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. | Version 1.0 | |||
| Metabolomics (LCMS, GCMS) |
Root polar
Seed Nonpolar Seed polar Control Water Stressed |
Nguyen Lab (unpublished) | Version 1.0 | |||
| Metabolomics (GCMS) | Root Hair and Stripped Root Heat Stress Time Points |
0hr 25C root hair
0hr 40C root hair 24hr 25C root hair 24hr 40C root hair 0hr 25C stripped roots 0hr 40C stripped roots 24hr 25C stripped roots 24hr 40C stripped roots |
Stacey Lab (unpublished) | Version 1.0 | ||
| 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. | Version 1.0 | |||
| 5' RATE |
Root Controlled
Root Stressed |
Nguyen Lab (unpublished) | Version 1.0 | |||
| Full length cdna |
Drought
Inoculation |
Stacey Lab (unpublished)
Nguyen Lab (unpublished) |
Version 1.0 | |||
| miRNA (Dataset -> 1) |
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. | Version 1.0 | |||
| miRNA (Dataset -> 2) |
Nodule miRNA |
Nod10_1 | Nod10_2 | Nod10_3
Nod15_1 | Nod15_2 | Nod15_3 Nod20_1 | Nod20_2 | Nod20_3 Nod25_1 | Nod25_2 | Nod25_3 Nod30_1 | Nod30_2 | Nod30_3 |
Stacey Lab (unpublished) | Version 1.0 | ||
| miRNA (Dataset -> 3) |
Roothair miRNA |
RH12_inoculated_1 | RH12_uninoculated_1
RH18_inoculated_1 | RH18_uninoculated_1 RH24_inoculated_1 | RH24_uninoculated_1 RH48_inoculated_1 | RH48_uninoculated_1 RH12_inoculated_2 | RH12_uninoculated_2 RH18_inoculated_2 | RH18_uninoculated_2 RH24_inoculated_2 | RH24_uninoculated_2 RH48_inoculated_2 | RH48_uninoculated_2 RH12_inoculated_3 | RH12_uninoculated_3 RH18_inoculated_3 | RH18_uninoculated_3 RH24_inoculated_3 | RH24_uninoculated_3 RH48_inoculated_3 | RH48_uninoculated_3 |
Stacey Lab (unpublished) | Version 1.0 | ||
| miRNA Target PARE Library_1 | Nodule miRNA PARE |
10DNod_s | 10DNod_l
15DNod_s | 15DNod_l 20DNod_s | 20DNod_l 25DNod_s | 25DNod_l 30DNod_s | 30DNod_l |
Stacey Lab (unpublished) | Version 1.0 | ||
| miRNA Target PARE Library_2 | Roothair miRNA PARE |
Root1_s | Root1_l
Seed_s | Seed_l Roothair1_s | Roothair1_l Roothair2_s | Roothair2_l Roothair3_s | Roothair3_l Roothair4_s | Roothair4_l Roothair5_s | Roothair5_l Roothair6_s | Roothair6_l Roothair7_s | Roothair7_l Roothair8_s | Roothair8_l |
Stacey Lab (unpublished) | Version 1.0 | ||
| 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. | Version 1.0 | |||
| SNP | Magellan vs PI567516C | Nguyen Lab (unpublished) | Version 1.0 | |||
| SNP | 41 NAM parents | Bilyeu Lab (unpublished) | Version 1.0 | |||
| SNP | SNP50K Array | Song Q1, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, Cregan PB. Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS One. 2013; 8(1):e54985. doi: 10.1371/journal.pone. 0054985. Epub 2013 Jan 25. | Version 1.0 | |||
| 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. | Version 1.0 | |||
| 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. | Version 1.0 | |||
| G.Soja | SNP, Inversion/Deletion | Kim MY, Lee S, Van K, Kim TH, Jeong SC, Choi IY, Kim DS, Lee YS, Park D, Ma J, Kim WY, Kim BC, Park S, Lee KA, Kim DH, Kim KH, Shin JH, Jang YE, Kim KD, Liu WX, Chaisan T, Kang YJ, Lee YH, Kim KH, Moon JK, Schmutz J, Jackson SA, Bhak J, Lee SH. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome.Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22032-7. Epub 2010 Dec 3. | Version 1.0 | |||
| GWAS (32 genomes from BGI) |
Wild and Cultivated Soybean | SNP,Insertion/Deletion | Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun SS, Zhang G. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet. 2010 Dec;42(12):1053-9. Epub 2010 Nov 14. | Version 1.0 | ||
| Small RNA Data |
Tag
seg_length sequence dcl4s_mutant_leaf_13_rep1 dcl4s_mutant_leaf_48_rep2 wide_type_leaf_37_rep1 wide_type_leaf_47_rep2 p_value |
Stacey Lab (unpublished) | Version 1.0 | |||
| Korean Lines |
A01 Sowon A02 Pureun A03 Kwangkyo A04 Ilpumgeomjeong A05 Seoritae A06 PI96983 A07 Haman A08 Geomjeongol A09 Hwangkeum A10 Williams82 Gsoja IT182932 B01 IT162825 B02 IT178480 B03 IT182869 B04 IT182840 B05 IT182848 |
SNP | Chung WH1, Jeong N, Kim J, Lee WK, Lee YG, Lee SH, Yoon W, Kim JH, Choi IY, Choi HK, Moon JK, Kim N, Jeong SC. Population Structure and Domestication Revealed by High-Depth Resequencing of Korean Cultivated and Wild Soybean Genomes. DNA Res. 2013 Nov 21. [Epub ahead of print] | Version 1.0 |