Assays

This list the version of packages installed as we have observed issues related to the use of the most current version of some python packaged for example scipy

Submitter: Uriel Urquiza Garcia

Biological problem addressed: Gene Expression

Investigation: Absolute units for proteins in Arabidopsis cloc...

Study: Reproducibility documentation

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 4th Oct 2022 at 08:48, Last updated: 19th Dec 2024 at 11:28

Gatway maps of genomic regions of clock genes

Millar group

Maps of cloned genes for rescuing selected clock mutants

Submitter: Uriel Urquiza Garcia

Assay type: Transformation

Technology type: Technology Type

Investigation: Absolute units for proteins in Arabidopsis cloc...

Study: Construction of NanoLUC-tagged plants

Organisms: Arabidopsis thaliana, Escherichia coli

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 21st Jan 2023 at 12:54, Last updated: 19th Dec 2024 at 11:28

promoter binding affinity calculations on the genome based on PBMs and EMA for CCA1 and LUX

Millar group

The promoter regions for clock genes that present a ChIP-seq signal were extracted from TAIR10 using costume python scripts using the gene list for Kamioka et al CCA1 or Daphne Ezer et al for LUX. The promoter was considered from the TSS of the gene until the annotated end of the upstream gene. Then, this region was scanned using the Energy Matrix derived using EMA working as a classifier for bound or unbound. After classification the calibrated PBM data calibrated using in vitro data was used ...

Submitter: Uriel Urquiza Garcia

Biological problem addressed: Model Analysis Type

Investigation: Absolute units for proteins in Arabidopsis cloc...

Study: Estimating DNA-binding affinities for Arabidops...

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: CCA1 PBM E-score data Franco-Zorrilla et al, CCA1 ensemble of matrices, CCA1 peaks from Kamioka et al, LUX E-scores data from Helfer et al, LUX ensemble of matrices, LUX peaks Ezer et al

Snapshots: No snapshots

Created: 25th Aug 2024 at 13:45, Last updated: 19th Dec 2024 at 11:28

Selection of complemented transgenic lines

Millar group

(Show All)

The reporter fusion constructs expressing clock proteins fused to NanoLUC or firefly FLUC were transformed into the cognate, clock-mutant host plants. Each host also contained a transcriptional FLUC fusion that was used to score the circadian period of each transgenic line in constant light. Transformants that expressed a functionally normal level of clock protein were selected by choosing lines that complemented the mutant's period defect back close to the wild type period. Note that the reporters ...

Submitter: Andrew Millar

Assay type: Transcriptional reporter gene

Technology type: Imaging

Investigation: Absolute units for proteins in Arabidopsis cloc...

Study: Construction of NanoLUC-tagged plants

Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type) (batch), Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm) (batch)

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 28th Aug 2024 at 18:21, Last updated: 19th Dec 2024 at 11:28

Reproducibility tool set

Millar group

This section contains the links to the tools used for reproducing the computational results presented in Urquiza-Garcia et al. 2022. This is required in particular because the SloppyCell model optimisation software is at some risk. Using Docker we can assure persistence for the computational environment that allows you to run SloppyCell.

The associated git repository can be found in https://hub.docker.com/r/uurquiza/urquiza2019a_tellurium_sloppycell/tags which can be cloned.

The docker image can ...

Submitter: Andrew Millar

Biological problem addressed: Model Analysis Type

Investigation: Absolute units for proteins in Arabidopsis cloc...

Study: Recalibrating the clock models for absolute pro...

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 9th Aug 2022 at 08:50, Last updated: 19th Dec 2024 at 11:28