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| Status |
Public on Jan 28, 2023 |
| Title |
Differential Nodal level promotes mesendoderm cell fate segregation mediated by chromatin organization |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Purpose: To investigate the mechanism of prechordal plate and anterior endoderm separation .
Methods: Nodal injected explants (injected with 10pg ndr2 mRNA) constructed from lft1 mutants and ndr1 morphants were harvested at 6hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 (10x Genomics, PN-1000075) according to the manufacturer’s protocol for 10000 cells recovery. For single-cell multiomics, zebrafish embryos at 6 hpf were harvested. Libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, 4 rxns PN-1000285) according to the manufacturer’s protocol for 10000 cells recovery.
Results: A total of 10,614 single-cell transcriptomes and 4,335 multiomics were collected after stringent quality control measures.
Conclusions: A slight bias in Nodal signaling promotes a differential chromatin structure between prechordal plate and endoderm, which drives a differential expression of those key regulators, such as gsc and ripply1 in these two cell lineages, and further regulates mesendoderm cell fate separation.
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| Overall design |
zebrafish Nodal explants constructed from lft1 mutants and ndr1 morphants were harvested at 6hpf for scRNA-seq. Zebrafish embryos were harvested at 6hpf for single-cell multiomics.
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| Contributor(s) |
Cheng T, Liu X |
| Citation missing |
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| |
| Submission date |
Jan 24, 2023 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Tao cheng |
| E-mail(s) |
11818118@zju.edu.cn
|
| Phone |
0571-88208276
|
| Organization name |
Zhejiang University
|
| Department |
Institute of genetics
|
| Street address |
886 Yuhangtang Road
|
| City |
Hang Zhou |
| State/province |
Zhe Jiang |
| ZIP/Postal code |
310000 |
| Country |
China |
| |
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| Platforms (1) |
| GPL24995 |
Illumina NovaSeq 6000 (Danio rerio) |
|
| Samples (4)
|
| GSM6969675 |
zebrafish Nodal explants constructed from lft1 mutants |
| GSM6969676 |
zebrafish Nodal explants constructed from ndr1 morphants |
| GSM6969677 |
zebrafish_embryo_multiomics_expression |
|
| Relations |
| BioProject |
PRJNA927004 |
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