 |
|
|
Microarray Data
Supported by:
NSF IOS-0618292, NSF2010: MAPK Cascade Signaling Networks
NSF MCB-0446109, Calcium-Dependent Protein Kinases in Plant Defense Signaling
NSF IOS_0843244, Arabidopsis 2010: Regulatory Mechanisms of Energy Signaling
|
|
|
|
Summary
We have performed functional analyses of 64 MAPKKKs, 10 MAPKKs, 20 MAPKs, 34 CDPKs and KIN10/11 to identify the Arabidopsis protein kinases (PKs) that play critical roles in the primary responses of plant signaling networks stimulated by hormones, abiotic stress, microbial-associated molecular patterns (MAMPs), bacterial effectors and energy status. Global gene expression profiles generated using the Affymetrix ATH1 GeneChips (22,500 probe sets representing approximately 24,000 Arabidopsis genes) have enabled the establishment of complex genomic links from diverse signals through PK cascades to thousands of primary target genes. We are providing the original (.CEL files) and processed (Excel files using RMA program, http://www.bioconductor.org/) microarray data (click the file to download) that have been processed in our lab for functional genomic projects on MAPK cascades, CDPK signaling and energy regulation. Our efforts have been focused on the primary responses occurring within the first hour of signaling initiation when PK activities are triggered and responsible for numerous and diverse downstream events. |
| |
| |
Data List
Flg22 Data
CDPK Data
KIN10 Data
MKK Data (in preparation)
Abiotic Stress Data (NASCArrays, AtGenExpress)
Hormone Data (NASCArrays, AtGenExpress)
MAMP Data (NASCArrays, AtGenExpress)
Pathogen Infection Data (NASCArrays, AtGenExpress)
Arabidopsis Microarray Databases
TAIR
NASCArrays
NCBI GEO
ArrayExpress
|
| |
| |
Useful websites to view global gene expression patterns
BAR (The Bio-Array Resource for Plant Functional Genomics)
AVT (AtGenExpression Visualization Tool)
Genevestigator
|
|
|
| Flg22 Data (GEO accession number GSE16557)
| Boudsocq, M., Willman, M., McCormack, M., Lee, H., Shan, L., He., P., Bush, J., Cheng, S.H., Sheen, J. 2010. Differential innate immune signalling via Ca2+ sensor protein kinases. Nature. In press |
| |
| Sample |
time |
treatment |
tissue |
conditions |
CEL file (raw data) |
Processed Data (in Excel) |
| control_p1 |
|
none |
protoplasts made from 5th-7th leaves of 28 day old plants (Col), 13 hr light, 11 hr dark; 60% humidity, 22oC |
2x105 cells, 5 ml WI (100 x 20 mm plate. Protoplasts pre-incubated at room temperature for 4 hr and then incubated at 28oC in the absence of flg22. |
CEL file |
|
| flg22_30min_p1 |
30 min |
100 nM flg22 |
protoplasts made from 5th-7th leaves of 28 day old plants (Col), 13 hr light, 11 hr dark; 60% humidity, 22oC |
2x105 cells, 5 ml WI (100 x 20 mm plate). Protoplasts pre-incubated at room temperature for 4 hr and then incubated at 28oC in the presense of flg22 |
CEL file |
RMA_cyber-T processed data in Excel |
| flg22_60min_p1 |
60 min |
100 nM flg22 |
protoplasts made from 5th-7th leaves of 28 day old plants (Col), 13 hr light, 11 hr dark; 60% humidity, 22oC |
2x105 cells, 5 ml WI (100 x 20 mm plate). Protoplasts pre-incubated at room temperature for 4 hr and then incubated at 28oC in the presense of flg22 |
CEL file |
RMA_cyber-T processed data in Excel |
| control_p2 |
|
none |
protoplasts made from 5th-7th leaves of 28 day old plants (Col), 13 hr light, 11 hr dark; 60% humidity, 22oC |
2x105 cells, 5 ml WI (100 x 20 mm plate. Protoplasts pre-incubated at room temperature for 4 hr and then incubated at 28oC in the absence of flg22. |
CEL file |
|
| flg22_30min_p2 |
30 min |
100 nM flg22 |
protoplasts made from 5th-7th leaves of 28 day old plants (Col), 13 hr light, 11 hr dark; 60% humidity, 22oC |
2x105 cells, 5 ml WI (100 x 20 mm plate). Protoplasts pre-incubated at room temperature for 4 hr and then incubated at 28oC in the presense of flg22 |
CEL file |
RMA_cyber-T processed data in Excel |
| flg22_60min_p2 |
60 min |
100 nM flg22 |
protoplasts made from 5th-7th leaves of 28 day old plants (Col), 13 hr light, 11 hr dark; 60% humidity, 22oC |
2x105 cells, 5 ml WI (100 x 20 mm plate). Protoplasts pre-incubated at room temperature for 4 hr and then incubated at 28oC in the presense of flg22 |
CEL file |
RMA_cyber-T processed data in Excel |
| control_sd1 |
|
none |
seedlings (Col) grown for 8 days in MS liquid medium (0.5xMS, 0.5% Sucrose, 1 ml in 6-well plates, 5 seedlings per well, no shaking). 13 h light: 11 h dark, 60% humidity, 22oC/19oC day/night temperature and 70 uE m-2s-1 light. |
|
CEL file |
|
| flg22_30min_sd1 |
30 min |
2 nM flg22 |
seedlings (Col) grown for 8 days in MS liquid medium (0.5xMS, 0.5% Sucrose, 1 ml in 6-well plates, 5 seedlings per well, no shaking). 13 h light: 11 h dark, 60% humidity, 22oC/19oC day/night temperature and 70 uE m-2s-1 light. |
Treated with DEX for 2 days then with flg22. |
CEL file |
RMA_cyber-T processed data in Excel |
| flg22_60min_sd1 |
60 min |
2 nM flg22 |
seedlings (Col) grown for 8 days in MS liquid medium (0.5xMS, 0.5% Sucrose, 1 ml in 6-well plates, 5 seedlings per well, no shaking). 13 h light: 11 h dark, 60% humidity, 22oC/19oC day/night temperature and 70 uE m-2s-1 light. |
Treated with DEX for 2 days then with flg22. |
CEL file |
RMA_cyber-T processed data in Excel |
| control_sd2 |
|
none |
seedlings (Col) grown for 8 days in MS liquid medium (0.5xMS, 0.5% Sucrose, 1 ml in 6-well plates, 5 seedlings per well, no shaking). 13 h light: 11 h dark, 60% humidity, 22oC/19oC day/night temperature and 70 uE m-2s-1 light. |
|
CEL file |
|
| flg22_30min_sd2 |
30 min |
2nM flg22 |
seedlings (Col)grown for 8 days in MS liquid medium (0.5xMS, 0.5% Sucrose, 1 ml in 6-well plates, 5 seedlings per well, no shaking). 13 h light: 11 h dark, 60% humidity, 22oC/19oC day/night temperature and 70 uE m-2s-1 light. |
Treated with DEX for 2 days then with flg22. |
CEL file |
RMA_cyber-T processed data in Excel |
| flg22_60min_sd2 |
60 min |
2nM flg22 |
seedlings (Col) grown for 8 days in MS liquid medium (0.5xMS, 0.5% Sucrose, 1 ml in 6-well plates, 5 seedlings per well, no shaking). 13 h light: 11 h dark, 60% humidity, 22oC/19oC day/night temperature and 70 uE m-2s-1 light. |
Treated with DEX for 2 days then with flg22. |
CEL file |
RMA_cyber-T processed data in Excel |
back to top
|
|
| CDPK Data (GEO accession number GSE16557)
| Boudsocq, M., Willman, M., McCormack, M., Lee, H., Shan, L., He., P., Bush, J., Cheng, S.H., Sheen, J. 2010. Differential innate immune signalling via Ca2+ sensor protein kinases. Nature. In press |
| |
| Sample |
time |
tissue |
conditions |
CEL file (raw data) |
Processed Data |
| control_1 |
6 hrs |
protoplasts made from 5th-7th leaves of 4 week old plants (Col) |
2x105 cells in 5 ml WI (100 x 20 mm plate). Transfected cells incubated for 6 hr at 25oC |
CEL file |
|
| CPKa5_1 |
6 hrs |
protoplasts made from 5th-7th leaves of 4 week old plants (Col) |
2x105 cells in 5 ml WI (100 x 20 mm plate). Transfected cells incubated for 6 hr at 25oC |
CEL file |
Processed data in Excel |
| CPKa11_1 |
6 hrs |
protoplasts made from 5th-7th leaves of 4 week old plants (Col) |
2x105 cells in 5 ml WI (100 x 20 mm plate). Transfected cells incubated for 6 hr at 25oC |
CEL file |
Processed data in Excel |
| control_2 |
6 hrs |
protoplasts made from 5th-7th leaves of 4 week old plants (Col) |
2x105 cells in 5 ml WI (100 x 20 mm plate). Transfected cells incubated for 6 hr at 25oC |
CEL file |
|
| CPKa5_2 |
6 hrs |
protoplasts made from 5th-7th leaves of 4 week old plants (Col) |
2x105 cells in 5 ml WI (100 x 20 mm plate). Transfected cells incubated for 6 hr at 25oC |
CEL file |
Processed data in Excel |
| CPKa11_2 |
6 hrs |
protoplasts made from 5th-7th leaves of 4 week old plants (Col) |
2x105 cells in 5 ml WI (100 x 20 mm plate). Transfected cells incubated for 6 hr at 25oC |
CEL file |
Processed data in Excel |
back to top
|
|
| KIN10 Data (GEO accession number GSE8257)
| Baena-González, E., Rolland, F., Thevelein, J., Sheen, J. 2007. A central integrator of transcription networks in plant stress and energy signalling. Nature, 448: 938-942.
|
| |
| Sample |
time |
tissue |
conditions |
CEL file (raw data) |
Processed Data |
| control_1 |
6 hr |
protoplasts isolated from the 5th and 6th leaves of 4 week old plants (Col). |
1.5x106 cells transfected with 1mg of control plasmid DNA and incubated in 10 ml WI buffer in a 150 x 15 mm plate |
CEL file |
GCOS processed data in Excel |
| control_2 |
6 hr |
protoplasts isolated from the 5th and 6th leaves of 4 week old plants (Col). |
1.5x106 cells transfected with 1mg of control eplasmid DNA and incubated in 10 ml WI buffer in a 150 x 15 mm plate |
CEL file |
GCOS processed data in Excel |
| KIN10_1 |
6 hr |
protoplasts isolated from the 5th and 6th leaves of 4 week old plants (Col). |
1.5x106 cells transfected with 1mg of KIN10-expressing plasmid DNA and incubated in 10 ml WI buffer in a 150 x 15 mm plate |
CEL file |
GCOS processed data in Excel |
| KIN10_2 |
6 hr |
protoplasts isolated from the 5th and 6th leaves of 4 week old plants (Col). |
1.5x106 cells transfected with 1mg of KIN10-expressing plasmid DNA and incubated in 10 ml WI buffer in a 150 x 15 mm plate |
CEL file |
GCOS processed data in Excel |
back to top
|
| Abiotic Stress Data (NASCArrays, AtGenExpress)
| Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., D'Angelo, C., Bornberg-Bauer, E,. Kudla, J., Harter, K. 2007. The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 50: 347-363
|
| |
H2O2 Data NASCArrays
Maike C. Rentel, David Lecourieux, Fatma Ouaked, Sarah L. Usher, Lindsay Petersen, Haruko Okamoto, Heather Knight, Scott C. Peck, Claire S. Grierson, Heribert Hirt & Marc R. Knight 2004. OXL1 kinase is necessary for oxidative burst-mediated sgnalling in Arabidopsis. Nature 427: 858-861
|
| |
back to top |
|
| Hormone Data (NASCArrays, AtGenExpress)
| Goda, H., Sasaki, E., Akiyama, K., Maruyama-Nakashita, A., Nakabayashi, K., Li, W., Ogawa, M., Yamauchi, Y., Preston, J., Aoki, K,. Kiba, T., Takatsuto, S., Fujioka, S., Asami, T., Nakano, T., Kato, H., Mizuno, T., Sakakibara, H., Yamaguchi, S., Nambara, E., Kamiya, Y., Takahashi, H., Hirai, M.Y., Sakurai, T., Shinozaki, K., Saito, K., Yoshida, S., Shimada, Y. 2008. The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. Plant J. 55: 526-542.
|
| |
Salicylic Acid Data EMBL-EBI ArrayExpress
van Leeuwen, Hans; Kliebenstein, Daniel J.; West, Marilyn A.L.; Kim, Kyunga; van Poecke, Remco; Katagiri, Fumiaki; Michelmore, Richard W.; Doerge, Rebecca W.; St.Clair, Dina. 2007 Natural Variation among Arabidopsis thaliana Accessions for Transcriptome Response to Exogenous Salicylic Acid. Plant Cell 19(7):2099
Kliebenstein DJ, West MA, van Leeuwen H, Kim K, Doerge RW, Michelmore RW, St Clair DA. 2006 Genomic survey of gene expression diversity in Arabidopsis thaliana. Genetics :1179-89
|
| |
back to top
|
| MAMP Data NASCArrays, AtGenExpress
Gust, A.A., Biswas, R., Lenz, H.D., Rauhut, T., Ranf, S., Kemmerling, B., Götz, F., Glawischnig, E., Lee, J., Felix, G., Nürnberger, T. 2007. Bacteria-derived peptidoglycans constitute pathogen-associated molecular patterns triggering innate immunity in Arabidopsis. J Biol Chem 282: 32338-32348.
Qutob, D., Kemmerling, B., Brunner, F., Küfner, I., Engelhardt, S., Gust, A.A., Luberacki, B., Seitz, H.U., Stahl, D., Rauhut, T., Glawischnig, E., Schween, G., Lacombe, B., Watanabe, N., Lam, E., Schlichting, R., Scheel, D., Nau, K., Dodt, G., Hubert, D., Gijzen, M., Nürnberger, T. 2006. Phytotoxicity and innate immune responses induced by Nep1-like proteins. Plant Cell. 18: 3721-3744. |
Chitin Data GEO Datasets
Zhang B, Ramonell K, Somerville S, and Stacey G. Characterization of Early, Chitin-Induced Gene Expression in Arabidopsis. Mol Plant Microbe Interact. 2002 Sep;15(9):963-70.
|
| |
elf Data EMBL-EBI ArrayExpress
C. Zipfel, G. Kunze, D. Chinchilla, A. Caniard, J. Jones, T. Boller, and G. Felix Perception of the Bacterial PAMP EF-Tu by the Receptor EFR Restricts Agrobacterium-Mediated Transformation Cell, Volume 125, Issue 4, Pages 749-760
|
| |
back to top
|
| Pathogen Infection Data AtGenExpress
| Data provided by Birgit Kemmerling and Thorsten Nürnberger |
| P.infestans AtGenExpress |
| Data provided by Dierk Scheel, Frederic Brunner & Lore Westphal |
| B.cinerea Ausubel Lab |
Data provided by the Ausubel Lab
Simone Ferrari, Roberta Galletti, Carine Denoux, Giulia De Lorenzo, Frederick M. Ausubel, and Julia Dewdney 2007 Resistance to Botrytis cinerea Induced in Arabidopsis by Elicitors Is Independent of Salicylic Acid, Ethylene, or Jasmonate Signaling But Requires PHYTOALEXIN DEFICIENT3 Plant Physiology 144:367-379 |
back to top
|
| |