Data Sources
Data Type:
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
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