UPR multi-omics datasets
1. Transcriptomes in the plant UPR [species; genotype(s); condition; time-course; method; ER stress inducer; raw data availability]
Martínez, I. M., & Chrispeels, M. J. (2003). Genomic analysis of the unfolded protein response in Arabidopsis shows its connection to important cellular processes. The Plant Cell, 15(2), 561-576. [Arabidopsis; Col-0; adaptive ER stress; no; microarray; Tm and DTT; unknown]
Noh, S. J., Kwon, C. S., Oh, D. H., Moon, J. S., & Chung, W. I. (2003). Expression of an evolutionarily distinct novel BiP gene during the unfolded protein response in Arabidopsis thaliana. Gene, 311, 81-91. [Arabidopsis; Col-0; adaptive ER stress; no; microarray; Tm; unknown; unknown]
Kamauchi, S., Nakatani, H., Nakano, C., & Urade, R. (2005). Gene expression in response to endoplasmic reticulum stress in Arabidopsis thaliana. The FEBS journal, 272(13), 3461-3476. [Arabidopsis; Col-0; adaptive ER stress; no; microarray; AZC, DTT and Tm; unknown]
Iwata, Y., Sakiyama, M., Lee, M. H., & Koizumi, N. (2010). Transcriptomic response of Arabidopsis thaliana to tunicamycin-induced endoplasmic reticulum stress. Plant Biotechnology, 27(2), 161-171. [Arabidopsis; Col-0; adaptive ER stress; yes; microarray; Tm; unknown]
Mishiba, K. I., Nagashima, Y., Suzuki, E., Hayashi, N., Ogata, Y., Shimada, Y., & Koizumi, N. (2013). Defects in IRE1 enhance cell death and fail to degrade mRNAs encoding secretory pathway proteins in the Arabidopsis unfolded protein response. Proceedings of the National Academy of Sciences, 110(14), 5713-5718. [Arabidopsis; Col-0 and ire1a/b; adaptive ER stress; no; microarray; Tm; unknown]
Srivastava, R., Li, Z., Russo, G., Tang, J., Bi, R., Muppirala, U., ... & Howell, S. H. (2018). Response to persistent ER stress in plants: a multiphasic process that transitions cells from prosurvival activities to cell death. The Plant Cell, 30(6), 1220-1242. [maize; B73; persistent ER stress; yes; RNA-seq; Tm; NCBI GEO GSE111250]
Kim, J. S., Yamaguchi-Shinozaki, K., & Shinozaki, K. (2018). ER-anchored transcription factors bZIP17 and bZIP28 regulate root elongation. Plant physiology, 176(3), 2221-2230. [Arabidopsis; Col-0, bzip28/17, bzip17/60 and bzip28/60; adaptive ER stress; no; RNA-seq; AZC, DTT and Tm; NCBI GEO GSE100371]
Ko, D. K., & Brandizzi, F. (2022). Advanced genomics identifies growth effectors for proteotoxic ER stress recovery in Arabidopsis thaliana. Communications Biology, 5(1), 16. [Arabidopsis; Col-0, bzip28-2, and bzip60-2; ER stress recovery; yes; RNA-seq; Tm; NCBI GEO GSE146723]
2. TF-DNA interactomes in the plant UPR [species; gene(s) or protein(s); experimental system; method; ER stress inducer; raw data availability]
Zhang, S. S., Yang, H., Ding, L., Song, Z. T., Ma, H., Chang, F., & Liu, J. X. (2017). Tissue-specific transcriptomics reveals an important role of the unfolded protein response in maintaining fertility upon heat stress in Arabidopsis. The Plant Cell, 29(5), 1007-1023. [Arabidopsis; MYC-bZIP28; in vivo; ChIP-seq; heat stress; NCBI GEO GSE94146]
Srivastava, R., Li, Z., Russo, G., Tang, J., Bi, R., Muppirala, U., ... & Howell, S. H. (2018). Response to persistent ER stress in plants: a multiphasic process that transitions cells from prosurvival activities to cell death. The Plant Cell, 30(6), 1220-1242. [maize; ZmbZIP17 and ZmbZIP60; mesophyll protoplasts; ChIP-seq; non-stress; NCBI GEO GSE111001]
Ko, D. K., & Brandizzi, F. (2021). A temporal hierarchy underpins the transcription factor–DNA interactome of the maize UPR. The Plant Journal, 105(1), 254-270. [maize; ZmPRX1, ZmBiP2, ZmSAR1, ZmBI1, ZmbZIP60 and ZmCP1; yeast; eY1H; non applicable; click to download]
Ko, D. K., & Brandizzi, F. (2022). Advanced genomics identifies growth effectors for proteotoxic ER stress recovery in Arabidopsis thaliana. Communications Biology, 5(1), 16. [Arabidopsis; GFP-bZIP28, and GFP-ZIP60; in vivo; ChIP-seq; Tm; NCBI GEO GSE146723]
Ko, D. K., & Brandizzi, F. (2022). Transcriptional competition shapes proteotoxic ER stress resolution. Nature plants, 8(5), 481-490. [Arabidopsis; YPet-GBF2; in vivo; ChIP-seq; Tm; NCBI BioProject PRJNA810750]
Ko, D. K., & Brandizzi, F. (2022). Transcriptional competition shapes proteotoxic ER stress resolution. Nature plants, 8(5), 481-490. [Arabidopsis; BiP3, bZIP28 and bZIP60; yeast; eY1H; non applicable; click to download]
3. Network-level resources in the plant UPR [species; network type; source data type; Cytoscape network file]
Ko, D. K., & Brandizzi, F. (2021). A temporal hierarchy underpins the transcription factor–DNA interactome of the maize UPR. The Plant Journal, 105(1), 254-270. [maize; GRNs; eY1H and RNA-seq; click to download]
Ko, D. K., & Brandizzi, F. (2022). Advanced genomics identifies growth effectors for proteotoxic ER stress recovery in Arabidopsis thaliana. Communications Biology, 5(1), 16. [Arabidopsis; GRNs; RNA-seq and ChIP-seq; click to download]
Ko, D. K., & Brandizzi, F. (2022). Transcriptional competition shapes proteotoxic ER stress resolution. Nature plants, 8(5), 481-490. [Arabidopsis; GRNs; eY1H and RNA-seq; click to download]