|
| Status |
Public on Sep 11, 2023 |
| Title |
Single-plant-omics reveals the cascade of transcriptional changes during the vegetative-to-reproductive transition |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Genome variation profiling by high throughput sequencing
|
| Summary |
A population of wild type plants can contain individuals with drastically different flowering times, due to developmental asynchrony. We performed RNA-seq on individual plants from a large population of wild type (Ws-2) Arabidopsis thaliana, sampling a large number (~70) of replicates at one timepoint during the flowering transition. We have characterised a major transcriptomic switch between plants before and after bolting. Applying methods used in single-cell RNA-seq, we used this data to order the plants by their predicted age – which is referred to as a pseudo-time series. In contrast to a traditional RNA-seq time series, this allows us to view changes in gene expression at a fine temporal scale. Importantly, we can infer the order that transcription factors ‘switch on’ during the vegetative to floral transition.
|
| |
|
| Overall design |
A population of wild type plants were grown under controlled conditions and physiological traits were measured. 75 plants were chosen for sequencing, to represent a diversity of bolting statuses.
We then performed RNA-seq and quantified the gene expression of each individual set of plant leaves.
In addition, we called variants across the population from the RNA-seq data, to assess the impact of genetic variation on physiology and developmental asynchrony.
|
| Web link |
https://www.biorxiv.org/content/10.1101/2023.09.11.557157v1
|
| |
|
| Contributor(s) |
Redmond EJ, Ronald J, Davis SJ, Ezer D |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Sep 07, 2023 |
| Last update date |
Mar 25, 2024 |
| Contact name |
Ethan James Redmond |
| E-mail(s) |
ethan.redmond@york.ac.uk
|
| Organization name |
University of York
|
| Department |
Department of Biology
|
| Lab |
Ezer lab
|
| Street address |
Wentworth Way
|
| City |
York |
| ZIP/Postal code |
YO10 5DD |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
|
| Samples (71)
|
|
| Relations |
| BioProject |
PRJNA1014093 |
Less...
More...