Visitors   Views   Downloads

The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula

View preprint
RT @GojThomson: Here is my preprint on the change in the global gene expression accompanying photoperiodic flowering time in Medicago @Peej…
RT @GojThomson: Here is my preprint on the change in the global gene expression accompanying photoperiodic flowering time in Medicago @Peej…
Here is my preprint on the change in the global gene expression accompanying photoperiodic flowering time in Medicago @PeejPreprints #flowering #plantscience #legume #RNAseq https://t.co/Hr6rmbWnPx
The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula https://t.co/kz3Umzip4a Photoperiodic flowering aligns plant reproduction to favourable seasons of the year to maximise successful production of seeds and…
NOT PEER-REVIEWED
"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

A peer-reviewed article of this Preprint also exists.

View peer-reviewed version

Supplemental Information

README

This is a key to the supplementary tables 1-9.

DOI: 10.7287/peerj.preprints.27366v1/supp-1

TPM

Gene abundances in Transcripts per Million for each gene by condition, timepoint and replicate

DOI: 10.7287/peerj.preprints.27366v1/supp-2

RT-qPCR Primers

Primers used for RT-qPCR in this study.

DOI: 10.7287/peerj.preprints.27366v1/supp-3

Individual timepoint analysis

Contrasts LD expression against SD expression results at individual timepoints using using Wald significance tests.

DOI: 10.7287/peerj.preprints.27366v1/supp-4

DE pattern genes

Results of the likelihood ratio test testing for genes with significant interaction terms indicative of differential patterns of expression.

DOI: 10.7287/peerj.preprints.27366v1/supp-5

DE pattern contrasts

Contrasts LD expression against SD expression for genes with differential patterns of expression at individual timepoints.

DOI: 10.7287/peerj.preprints.27366v1/supp-6

DE pattern clusters

Cluster assignments of genes of the differential patterns of expression class

DOI: 10.7287/peerj.preprints.27366v1/supp-7

DE magnitude genes

Results of the Wald significance test testing for the significance of the condition in explaining the magnitude of gene expression.

DOI: 10.7287/peerj.preprints.27366v1/supp-8

DE magnitude contrasts

Contrasts LD expression against SD expression for genes with differential magnitudes but not patterns of expression at individual timepoints.

DOI: 10.7287/peerj.preprints.27366v1/supp-9

DE magnitude clusters

Cluster assignments of genes with differential magnitudes but not patterns of expression at individual timepoints

DOI: 10.7287/peerj.preprints.27366v1/supp-10

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Geoffrey Thomson conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

James Taylor performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

Joanna Putterill conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

The University of Auckland Institutional Biological Safety Committee granted Biological Safety Approval to carry out this study within its facilities. (GMO08-UA006).

Data Deposition

The following information was supplied regarding data availability:

Raw data:

GEO: Gene Expression Omnibus - GSE118893

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118893

Code:

Figshare repository

DOI: 10.17608/k6.auckland.6993641.v5

https://figshare.com/articles/Thomson_et_al_2018_SDtoLDShiftAnalysis/699364

Funding

The research was funded by C10X0816 MeriNET (www.msi.govt.nz/) and by the New Zealand Marsden Fund (http://www.royalsociety.org.nz/programmes/funds/marsden/) contract 14-UOA-125. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Some Markdown syntax is allowed: _italic_ **bold** ^superscript^ ~subscript~ %%blockquote%% [link text](link URL)
 
By posting this you agree to PeerJ's commenting policies