Spreadsheet: 6a869cd5-fa86-4a35-9bfd-d37131e9aef4
Sheet: Sheet1

Unnamed: 0 | Lit_S_down | Lit_S_up | Tamaokai_12h | Fowler_0.5-8h | Kreps_3h | Chen_3h | Seki_1-2h | Seki_5h | Seki_10h | Vogel-P_1h | Vogel-S_1h | Knight_3h | Chinnusamy_6h | AtGE_0.5h | AtGE_1h | AtGE_3h | AtGE_6h | AtGE_12h | Lit_M_down | [NAME] | Fowler_24h | Kreps_27h | Chen_27h | Seki_24h | Vogel-P_24h | Vogel-S_24h | Bramke_24h | Warren_24h | AtGE_24h | Lit_L_down | Lit_L_up | Jung_3d | Fowler_7d | Vogel-P_7d | Vogel-S_7d | [NAME] | Unnamed: 37 | Unnamed: 38 | Unnamed: 39 | MWG_ACC-NA
Growth | - |  | rockwool | plate | hydroponic |  | plate |  |  | plate | soil | plate | plate | hydroponic |  |  |  |  | - |  | plate | hydroponic |  | plate | plate | soil | soil | plate | hydroponic | - |  | soil | plate | plate | soil | soil |  |  |  | soil
Age | - |  | 14 d | 11 d | 21 d |  | 21 d |  |  | 10 d | 18 d | 7 d | 10 d | 16 d |  |  |  |  | - |  | 11 d | 21 d |  | 21 d | 10 d | 18 d | 1.12 | 1.14 | 16 d | - |  | 21 d | 11 d | 10 d | 18 d | 43-46 d |  |  |  | 43-46 d
Time | <12 h |  | 12 h | 0.5-8 h | 3 h |  | 1-10 h |  |  | 1 h | 1 h | 3 h | 6 h | 0.5-12 h |  |  |  |  | 24-48 h |  | 24 h | 27 h |  | 24 h | 24 h | 24 h | 24 h | 24 h? | 24 h | >48 h |  | 3 d | 7 d | 7 d | 7 d | 14 d |  |  |  | 14 d
Photoperiod | - |  | 14/10 | 24/0 | 12/12 |  | 16/8 |  |  | 24/0 | 24/0 | 24/0? | 24/0 | 16/8 |  |  |  |  | - |  | 24/0 | 12/12 |  | 16/8 | 24/0 | 24/0 | 8/16 | 24/0 | 16/8 | - |  | 24/0 | 24/0 | 24/0 | 24/0 | 16/8 |  |  |  | 16/8
Light intensity (µE m-2 s-1) | - |  | 50 | 20-40 | 75 |  | 0.7-0.8 |  |  | 25 | 25 | 80 | 30 | 40 |  |  |  |  | - |  | 20-40 | 75 |  | 0.7-0.8 | 25 | 25 | same as control | - | 40 | - |  | 100 | 20-40 | 25 | 25 | 90 |  |  |  | 90
Temperature | - |  | 4°C | 4°C | 4°C |  | 4°C |  |  | 4°C | 4°C | 5°C | 4°C | 4°C |  |  |  |  |  |  | 4°C | 4°C |  | 4°C | 4°C | 4°C | 4°C | 4°C | 4°C | - |  | 0°C | 4°C | 4°C | 4°C | 4°C |  |  |  | 4°C
Array | - |  | cDNA | AtGenome | AtGenome |  | RIKEN |  |  | ATH1 | ATH1 | ATH1 | ATH1 | ATH1 |  |  |  |  | - |  | AtGenome | AtGenome |  | RIKEN | ATH1 | ATH1 | ATH1 | ATH1 | ATH1 | - |  | SAGE | AtGenome | ATH1 | ATH1 | ATH1 |  |  |  | MWG
Replication | - |  | (1B-1T)x3 | (1B-1T)x2 | 2B-1T |  | 1B-1T |  |  | (1B-1T)x2 | (1B-1T)x2 | 1B-1T | 1B-1T | 1B-2T |  |  |  |  | - |  | (1B-1T)x2 | 2B-1T |  | 1B-1T | (1B-1T)x2 | (1B-1T)x2 | 2B-1T | (1B-1T) x2 | 1B-2T | - |  |  | (1B-1T)x2 | (1B-1T)x2 | (1B-1T)x2 | (1B-1T)x3 |  |  |  | (1B-2T)x3
Analysis | - |  | 2x | 2.5x | 2x |  | 2x |  |  | MAS5 | MAS5 | MAS5 | MAS5 | MAS5 |  |  |  |  | - |  | 2.5x | 2x |  | 2x | MAS5 | MAS5 | MAS5 | MAS5 | MAS5 | - |  | - | 2.5x | MAS5 | MAS5 | GCRMA, [NAME], < 0.05 fdr p-value |  |  |  | MAVI Pro, [NAME], < 0.05 fdr p-value
Data |  |  |  |  |  |  | [NAME] |  |  | http://arabidopsis.org/servlets/TairObject?type=hyb_descr_collection&id=[PHONE] | http://arabidopsis.org/servlets/TairObject?type=hyb_descr_collection&id=[PHONE] | http://affymetrix.arabidopsis.info/narrays/experimentpage.pl?experimentid=73 |  | http://www.arabidopsis.org/info/expression/ATGenExpress.jsp |  |  |  |  |  |  |  |  |  | [NAME] | http://arabidopsis.org/servlets/TairObject?type=hyb_descr_collection&id=[PHONE] | http://arabidopsis.org/servlets/TairObject?type=hyb_descr_collection&id=[PHONE] | http://affymetrix.arabidopsis.info/narrays/experimentpage.pl?experimentid=24 | http://affymetrix.arabidopsis.info/narrays/experimentpage.pl?experimentid=70 | http://www.arabidopsis.org/info/expression/ATGenExpress.jsp |  |  |  |  | http://arabidopsis.org/servlets/TairObject?type=hyb_descr_collection&id=[PHONE] | http://arabidopsis.org/servlets/TairObject?type=hyb_descr_collection&id=[PHONE]
Comments | The numbers in each column can be cross-referenced to a supporting publication in the supplemental table |  |  | Updated AGI mappings were used. | These studies use the same data but [NAME] only analyses transcription factors and uses a lower detection threshold. Updated AGI mappings were used. |  | 1.5 fold change at 1 h, 2 fold change at 2 h. |  |  |  |  |  | MAS5 analysis was provided in the paper and selection was based on this. | Duplicate biological samples were taken but as these were pooled from the same batch of plants this is considered technical replication. During affy quality control the 1 h replicate 1 was identified as an outlier with low raw values probably due to a technical artifact. This may slightly affect the number of significant changes. |  |  |  |  | See short. |  | Updated AGI mappings were used. | See short. |  |  |  |  |  | The duration of the cold treatment is not stated but is an estimate based on comparisons. | See short | See short. |  | [NAME] against NCBI NlaIII Arabidopsis libraries (11/08/04) http://www.ncbi.nlm.nih.gov/SAGE/index.cgi?cmd=tagsearch, those which matched multiple AGI codes are highlighted in green. | Updated AGI mappings were used.
Reference | Supplemental Table L |  | Tamaoki, M., Matsuyama, T., Nakajima, N., [NAME], M., Kubo, [NAME] and Saji, H. 2004. A method for diagnosis of plant environmental stresses by gene expression profiling using a cdna macroarray. Environmental Pollution 131: 137-145. | Fowler, S. and Thomashow, M. F. 2002. Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the cbf cold response pathway. Plant Cell 14: 1675-1690. | Kreps, J. A., [NAME], [NAME] [NAME], [NAME], Zhu, T., Wang, [NAME] and [NAME], J. F. 2002. Transcriptome changes for arabidopsis in response to salt, osmotic, and cold stress. Plant Physiology 130: 2129-2141. | [NAME], [NAME], Provart, [NAME], J., Katagiri, [NAME], [NAME], H.-S., Eulgem, T., [NAME], [NAME], Luan, S., Zou, [NAME], Whitham, S. A., Budworth, P. R., [NAME], [NAME], [NAME], [NAME], [NAME], Lam, S., Kreps, J. A., [NAME], J. F., Si-Ammour, A., [NAME], B., Heinlein, M., Kobayashi, K., [NAME], [NAME], [NAME], [NAME], Wang, [NAME] and Zhu, T. 2002. Expression profile matrix of arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant Cell 14: 559-574. | [NAME], M., Narusaka, M., [NAME], [NAME], Nanjo, T., Fujita, M., [NAME], Y., Kamiya, A., Nakajima, M., Enju, A., Sakurai, T., Satou, M., Akiyama, K., [NAME], T., Yamaguchi-Shinozaki, K., Carninci, P., Kawai, J., Hayashizaki, Y. and Shinozaki, K. 2002. Monitoring the expression profiles of 7000 arabidopsis genes under drought, cold and high-salinity stresses using a full-length cdna microarray. Plant Journal 31: 279-292. |  |  | Vogel, [NAME], [NAME], [NAME], [NAME], [NAME], [NAME], [NAME] and Thomashow, M. F. 2005. Roles of the [NAME] and zat12 transcription factors in configuring the low temperature transcriptome of arabidopsis. Plant Journal 41: 195-211. |  |  | Chinnusamy, V., Ohta, M., [NAME], [NAME], Lee, [NAME], Hong, [NAME], Agarwal, M. and Zhu, J. K. 2003. Ice1: A regulator of cold-induced transcriptome and freezing tolerance in arabidopsis. Genes & Development 17: 1043-1054. |  |  |  |  |  | Supplemental Table L |  | Fowler, S. and Thomashow, M. F. 2002. Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the cbf cold response pathway. Plant Cell 14: 1675-1690. | Kreps, J. A., [NAME], [NAME] [NAME], [NAME], Zhu, T., Wang, [NAME] and [NAME], J. F. 2002. Transcriptome changes for arabidopsis in response to salt, osmotic, and cold stress. Plant Physiology 130: 2129-2141. | [NAME], [NAME], Provart, [NAME], J., Katagiri, [NAME], [NAME], H.-S., Eulgem, T., [NAME], [NAME], Luan, S., Zou, [NAME], Whitham, S. A., Budworth, P. R., [NAME], [NAME], [NAME], [NAME], [NAME], Lam, S., Kreps, J. A., [NAME], J. F., Si-Ammour, A., [NAME], B., Heinlein, M., Kobayashi, K., [NAME], [NAME], [NAME], [NAME], Wang, [NAME] and Zhu, T. 2002. Expression profile matrix of arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant Cell 14: 559-574. | [NAME], M., Narusaka, M., [NAME], [NAME], Nanjo, T., Fujita, M., [NAME], Y., Kamiya, A., Nakajima, M., Enju, A., Sakurai, T., Satou, M., Akiyama, K., [NAME], T., Yamaguchi-Shinozaki, K., Carninci, P., Kawai, J., Hayashizaki, Y. and Shinozaki, K. 2002. Monitoring the expression profiles of 7000 arabidopsis genes under drought, cold and high-salinity stresses using a full-length cdna microarray. Plant Journal 31: 279-292. | Vogel, [NAME], [NAME], [NAME], [NAME], [NAME], [NAME], [NAME] and Thomashow, M. F. 2005. Roles of the [NAME] and zat12 transcription factors in configuring the low temperature transcriptome of arabidopsis. Plant Journal 41: 195-211. |  |  |  | See short. | Supplemental Table L |  | [NAME], [NAME], [NAME], [NAME] and [NAME], [NAME]. Use of sage technology to reveal changes in gene expression in arabidopsis leaves undergoing cold stress. Plant Molecular Biology 52: 553-567. | Fowler, S. and Thomashow, M. F. 2002. Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the cbf cold response pathway. Plant Cell 14: 1675-1690. | Vogel, [NAME], [NAME], [NAME], [NAME], [NAME], [NAME], [NAME] and Thomashow, M. F. 2005. Roles of the [NAME] and zat12 transcription factors in configuring the low temperature transcriptome of arabidopsis. Plant Journal 41: 195-211. |  | This study |  |  |  | This study