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Series GSE116004 Query DataSets for GSE116004
Status Public on Mar 18, 2019
Title Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary In Arabidopsis, a large subset of heat responsive genes exhibits diurnal or circadian oscillations. However, to what extent the dimension of time and/or the circadian clock contribute to heat stress responses remains largely unknown. To determine the direct contribution of time of day and/or the clock to differential heat stress responses, we probed wild-type and mutants of the circadian clock genes CCA1, LHY, PRR7, and PRR9 following exposure to heat (37°C) and moderate cold (10°C) in the early morning (ZT1) and afternoon (ZT6). Thousands of genes were differentially expressed in response to temperature, time of day, and/or the clock mutation. Approximately 30% more genes were differentially expressed in the afternoon compared to the morning, and heat stress significantly perturbed the transcriptome. Of the DEGs (~3000) specifically responsive to heat stress, ~70% showed time of day (ZT1 or ZT6) occurrence of the transcriptional response. For the DEGs (~1400) that are shared between ZT1 and ZT6, we observed changes to the magnitude of the transcriptional response. In addition, ~2% of all DEGs showed differential responses to temperature stress in the clock mutants. The findings in this study highlight a significant role for time of day in the heat stress responsive transcriptome, and the clock through CCA1 and LHY, appears to have a more profound role than PRR7 and PRR9 in modulating heat stress responses during the day. Our results emphasize the importance of considering the dimension of time in studies on abiotic stress responses in Arabidopsis.
 
Overall design We used RNA-sequencing to measure transcriptomic changes in Columbia-0 (WT), cca1-1/lhy-20 (cca1lhy) and prr7-3/prr9-1 (prr7prr9) under 1 h of moderate cold (10°C) and 1 h of heat stress (37°C). Samples were collected at ZT1 and ZT6.

Seedlings were grown on plates containing Murashige and Skoog (MS) medium supplemented with 1.5% sucrose (wt/vol) in 12 h light and 12 h dark (LD) cycles for 12 days at constant 22°C and 90 µm light intensity.

Single-end 75 base pair sequences were generated for each mRNA library using the NextSeq 500 (Illumina).
 
Contributor(s) Blair EJ, Bonnot T, Hummel M, Hay E, Marzolino JM, Quijada IA, Nagel DH
Citation(s) 30886204
Submission date Jun 19, 2018
Last update date Apr 02, 2019
Contact name Dawn Nagel
E-mail(s) dawnn@ucr.edu
Organization name University of Califonia, Riverside
Department Botany and Plant Sciences
Lab Dawn Nagel
Street address 3401 Watkins Avenue (Batchelor Hall Rm 1123)
City Riverside
State/province CA
ZIP/Postal code 92507
Country USA
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (35)
GSM3204821 Col-0_10C_ZT1_Rep2
GSM3204822 Col-0_10C_ZT1_Rep3
GSM3204823 Col-0_10C_ZT1_Rep4
Relations
BioProject PRJNA476778
SRA SRP150864

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE116004_cca1lhyData.xls.gz 19.5 Mb (ftp)(http) XLS
GSE116004_prr7prr9Data.xls.gz 18.1 Mb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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