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| Status |
Public on Sep 07, 2020 |
| Title |
Identification of genes regulated by the MADS transcription factor (TF), SEPALLATA3, in the context of the double sep1sep2 and triple sep1sep2sep3 mutant background, by RNA-Seq analysis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
These analyses allowed the identification of more than 2000 genes regulated by the MADS TF, SEPALLATA3 (SEP3). Although the involvement of SEP3 in all flower organ development is well established, the single sep3 mutant shows no flower phenotype, due to redundancy with other SEPALLATA genes. The triple mutant, sep1sep2sep3, shows no floral organ development except sepals, while the sep1sep2 mutant showed characteristic WT flower with, from the outer to the inner whorl of the flower, 4 sepals, 4 petals, 6 stamens and one gynoecium. We performed RNA-seq analysis on sep1sep2, sep1sep2sep3 and on sep1sep2sep3 lines complemented with SEP3 to highlight genes involved in floral organ development and controlled by SEP3. For this purpose we compared gene expression between the triple and the double mutant, and between triple mutant lines complemented with SEP3 and the triple mutant. Genes were considered regulated by SEP3 when the log FC was between 1 and -1 and the FDR <0.05. Using these criteria, we obtained a list of >2000 genes regulated by SEP3.
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| Overall design |
RNA seq analysis were performed on inflorescence meristem and flower buds up to stage 10-11 harvested from Arabidopsis plants grown in parralel in long days conditions. Experiments were performed on 2 replicates from sep1sep2 mutant, 2 replicates from sep1sep2sep3 triples mutant, and 2 independantes complemented lines expressing SEP3 in the sep1sep2sep3 background (considered as 2 replicats). These lines are described in Hugouvieux et al, Nucleic Acid Research, 2018:1;46(10):4966-4977. doi: 10.1093/nar/gky205. Libraries and sequencing were performed by Genewiz (Illumina High SEq, 2X150 bp configuration).
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| Contributor(s) |
Hugouvieux V, Lucas J, Zubieta C |
| Citation(s) |
32890394 |
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| Submission date |
May 14, 2020 |
| Last update date |
Sep 09, 2020 |
| Contact name |
Veronique Hugouvieux |
| E-mail(s) |
veronique.hugouvieux@cea.fr, vhugouvieux@gmail.com
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| Organization name |
CEA Grenoble
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| Department |
IRIG
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| Lab |
LPCV
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| Street address |
17 rue des Martyrs
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| City |
Grenoble |
| ZIP/Postal code |
38054 |
| Country |
France |
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| Platforms (1) |
| GPL21785 |
Illumina HiSeq 4000 (Arabidopsis thaliana) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA632895 |
| SRA |
SRP261666 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE150605_RAW.tar |
790.0 Kb |
(http)(custom) |
TAR (of TXT) |
| GSE150605_sep1sep2sep3-sep1sep2.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE150605_sep1sep2sep3_SEP3-sep1sep2ep3.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Raw data provided as supplementary file |
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