Clock gene RNAs under RD-RR in clock mutants, expt 3
Clock gene RNAs under RD-RR in clock mutants, expt 3
| Property | Value |
|---|---|
| BioDare ID | 13228357055348 |
| Author | Locke |
| Institution | |
| License |
Description
Literature data from: 'Extension of a genetic network model by iterative experimentation and mathematical analysis.' by: Locke.
First, heroic large-scale RNA profile screen by real-time qPCR in 96-well format, by Megan Southern in 2005. Experiment 3 of 4.
Purpose
Testing effects of clock gene mutants (gi-11, TOC1-ox, GI-ox) in the Ws accession, on clock gene RNA profiles, in order to identify hypothetical Y in Locke 2005 model.
Comments
curated by Andrew Millar, 2011. Data are noisy (especially TOC1, FT, CO, parts of ELF3) in part due to much manual pipetting. Note ACT2 normalisation differs in 3 and 4 from experiments 1 and 2, as only Ws accessions tested.
SEEK ID: https://fairdomhub.org/assays/2915
Experimental assay
Projects: BioDare1
Investigation: Flis Anna
Study: Flis et al. (2015)
Assay position:
Assay type: Experimental Assay Type
Technology type: Technology Type
Organisms: Arabidopsis thaliana
Export PNG
Download
Creators and Submitter
Views: 64
Created: 18th Jun 2026 at 12:36
Last updated: 18th Jun 2026 at 12:38
TagsThis item has not yet been tagged.
Related items
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
Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure
Flis et al. (2015)
DOI: 10.1098/rsob.150042
Submitter: Daniel Thedie
Investigation: Flis Anna
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, 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
MMS qRT-PCR primers and toc1-2 control (from BioDare)
STANDARD_DATAFILE.1 (from BioDare)
STANDARD_RAWDATAFILE.1 (from BioDare)
Expt3 for BioDare upload.1 (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
