|
| Status |
Public on Dec 18, 2020 |
| Title |
Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates |
| Organism |
Xenopus tropicalis |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We applied chromatin accessibility and single cell transcriptome analyses to explore the emergence of heterogeneity and underlying gene-regulatory mechanisms during early gastrulation in Xenopus. TF activity was inferred by integrating chromatin accessibility and single cell transcriptomics. Our results show that combinatorial activity of zygotically expressed transcription factors acts on maternally-regulated accessible chromatin to induce organizer gene expression.
|
| |
|
| Overall design |
ATAC-seq on Xenopus embryos (stage 9, 10.5, 12 and 16) and gastrula stage embryo explants (Animal cap and Dorsal marginal zone). RNA-seq on animal caps overexpressed with Foxb1, Foxb1 + Eomes, Eomes, Irx3, Irx3 + Otx2 and Lhx8 mRNA. ScRNA-seq on Animal cap and Dorsal marginal zone explants. scATAC-seq was performed on stage 10.5 Xenopus embryos.
|
| |
|
| Contributor(s) |
Bright AR, van Genesen S, Li Q, Grasso A, Veenstra GJ |
| Citation(s) |
33555045 |
| |
| Submission date |
Feb 20, 2020 |
| Last update date |
Mar 02, 2021 |
| Contact name |
Ann Rose Bright |
| Organization name |
RIMLS
|
| Department |
Department of Molecular Biology
|
| Street address |
Geert Grooteplein Zuid 30
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platforms (2) |
| GPL21875 |
Illumina HiSeq 2500 (Xenopus tropicalis) |
| GPL24884 |
Illumina NextSeq 500 (Xenopus tropicalis) |
|
| Samples (132)
|
|
| Relations |
| BioProject |
PRJNA607864 |
| SRA |
SRP250335 |
Less...
More...