Project description:To identify transcription factor (TF) genes exhibiting preferential expression during SE, expression profiles of 1,880 TFs were compared in two genotypes with largely different capacities for SE induction in IZE culture on auxin medium, namely the highly embryonic Col-0 accession and the tanmei mutant unable to form somatic embryos. Our study revealed 729 TFs whose expression changes during the 10-day incubation period of SE; 141 TFs displayed distinct differences in expression patterns in embryogenic versus non-embryogenic cultures. This study provides comprehensive data focused on the expression of TF genes during SE and provides guidelines for further research on functional genomics of SE. The experiment was designed to monitor the expression of 1,880 TF genes at three distinctive stages of IZE-derived embryogenic culture, which refer to: (i) freshly isolated explants competent to undergo embryogenic transition (0 d), (ii) explant tissue subjected to SE induction (5 d), and (iii) the advanced phase of embryogenesis related to somatic embryo formation (10 d).

2013-07-31 | E-GEOD-45697 | biostudies-arrayexpress

The Dynamic Proteome in Arabidopsis Thaliana Early Embryogenesis

Project description:Using nanoproteomics,we profiled the dynamics of proteome and found potentially important proteins in Arabidopsis thaliana early embryogenesis. Combining with RNAs-seq, we unveiled the relationship of protein and mRNA during Arabidopsis embryogenesis.

2022-03-03 | GSE197556 | GEO

Arabidopsis thaliana

Project description:Expression data from tissues during somatic embryogenesis in Arabidopsis

| PRJNA212312 | ENA

The embryonic transcriptome of Arabidopsis thaliana

Project description:Cellular differentiation is associated with changes in transcript populations. Accurate quantification of transcriptomes during development can thus provide global insights into differentiation processes including the fundamental specification and differentiation events operating during plant embryogenesis. However, multiple technical challenges have limited the ability to obtain high quality early embryonic transcriptomes, namely the low amount of RNA obtainable and contamination from surrounding endosperm and seed-coat tissues. We compared the performance of three low-input mRNA sequencing (mRNA-seq) library preparation kits on 0.1 to 5 nanograms (ng) of total RNA isolated from Arabidopsis thaliana (Arabidopsis) embryos and identified a low-cost method with superior performance. This mRNA-seq method was then used to profile the transcriptomes of Arabidopsis embryos across eight developmental stages. By comprehensively comparing embryonic and post-embryonic transcriptomes, we found that embryonic transcriptomes do not resemble any other plant tissue we analyzed. Moreover, transcriptome clustering analyses revealed the presence of four distinct phases of embryogenesis which are enriched in specific biological processes. We also compared zygotic embryo transcriptomes with publicly available somatic embryo transcriptomes. Strikingly, we found little resemblance between zygotic embryos and somatic embryos derived from late-staged zygotic embryos suggesting that somatic and zygotic embryo transcriptomes are distinct from each other. In addition to the biological insights gained from our systematic characterization of the Arabidopsis embryonic transcriptome, we provide a data-rich resource for the community to explore.

2018-12-21 | GSE121236 | GEO