Flis et al. TiMet clock gene comparison across photoperiods
Flis et al. TiMet clock gene comparison across photoperiods
| Property | Value |
|---|---|
| BioDare ID | 3967 |
| Author | Anna Flis |
| Institution | Max Planck Inst. Golm |
| License | CC_BY |
Description
Literature data from: 'Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis' by: Anna Flis.
Col plants were grown in soil under 6, 8, 12 and 18h photoperiod for 21 days, and duplicate samples were harvested at 2 h intervals though a 24 h cycle. qRT-PCR with absolute calibration to spiked-in standards returned RNA copy number per gramme Fresh Weight of rosette tissue. Cell number was separately estimated at 25,000,000 per gFW.
Purpose
TiMet clock gene expression profiles, baseline comparison across photoperiods in Col wild-type plants, under 6, 8, 12 and 18 h photoperiod. These data define the response of the clock genes under different photoperiods, where other analysis in the TiMet project studied proteome and metabolite levels. Absolute expression levels were compared, as RNA copies per gFW or per cell.
Comments
TiMet experiment WP1.2B. Data file "TiMet 1.2 - Photoperiod exp - metabolites and transcripts.xlsx;calculations" 2013
SEEK ID: https://fairdomhub.org/assays/2919
Experimental assay
Projects: BioDare1
Investigation: Flis Anna
Study: Flis et al. (2016)
Assay position:
Assay type: Experimental Assay Type
Technology type: Technology Type
Organisms: Arabidopsis thaliana
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Created: 18th Jun 2026 at 12:49
Last updated: 18th Jun 2026 at 12:50
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https://orcid.org/0000-0002-1352-7245Research Software Engineer in the Biological Research Data Management team (BioRDM) at the University of Edinburgh.
The Centre for Engineering Biology is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2023 as the successor to SynthSys, itself founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE). CSBE was newly founded in 2007. The Centre for Engineering Biology is a hub organisation that links across multiple, major funding awards, including an Engineering Biology Mission Hub, and EPSRC C-loop.
Projects: Millar group, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, TiMet, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository, BioDare1
Web page: https://biology.ed.ac.uk/centre-engineering-biology
Experiment data previously hosted on the original version of BioDare (biodare.ed.ac.uk).
Programme: Centre for Engineering Biology (prev. SynthSys)
Public web page: Not specified
Collection of experiments created by Flis Anna on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Flis et al. (2015), Flis et al. (2016), Unpublished
Assays: Clock gene RNAs under RD-RR in clock mutants, expt 1, Clock gene RNAs under RD-RR in clock mutants, expt 2, Clock gene RNAs under RD-RR in clock mutants, expt 3, Clock gene RNAs under RD-RR in clock mutants, expt 4, Flis et al. TiMet clock gene comparison across photoperiods, McWatters A.t. Col-0 WT clock RNA timeseries, Q-PCR LD (12:12) 17C CAB2, Q-PCR LD (12:12) 17C CCA1, Q-PCR LD (12:12) 17C ELF3, Q-PCR LD (12:12) 17C ELF4, Q-PCR LD (12:12) 17C GI, Q-PCR LD (12:12) 17C LHY, Q-PCR LD (12:12) 17C LUX, Q-PCR LD (12:12) 17C PRR5, Q-PCR LD (12:12) 17C PRR7, Q-PCR LD (12:12) 17C PRR9, Q-PCR LD (12:12) 17C TOC1, TiMet WP1.1 WS seedling vs rosette, TiMet WP1.1 qRT-PCR LD to LL and LD, TiMet WP1.1 qRT-PCR elf3 LD
Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis
Flis et al. (2016)
DOI: 10.1111/pce.12754
Submitter: Daniel Thedie
Investigation: Flis Anna
Assays: Flis et al. TiMet clock gene comparison across photoperiods
TiMet 1.2 - Photoperiod exp - transcripts AJMv2 for BioDare (from BioDare)
List of samples used in the assay (extracted from original BioDare metadata and converted to csv)
Original BioDare metadata, converted to json format
Readme file
