|
| Status |
Public on Jan 28, 2023 |
| Title |
zebrafish Nodal explants constructed from lft1 mutants |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish cells
|
| Organism |
Danio rerio |
| Characteristics |
strain: lft1 mutant
tissue: embryonic cells
age: 6hpf
|
| Treatment protocol |
10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at 128 cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage, then, were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 6hpf (corresponding to embryonic developmental stage).
|
| Growth protocol |
Explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 (10x Genomics, PN-1000075) and 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina sequencing reads were aligned to the zebrafish mRNA reference genome (GRCz11) using the 10x Genomics CellRanger pipeline (version 6.1.2) and cellranger-arc (version 2.0.0) with default parameters.
Assembly: GRCz11
Supplementary files format and content: tar archivr or gzip compressed files included filtered_gene_bc_matrices and ATAC fragments after running CellRanger or cellranger-arc pipeline.
|
| |
|
| Submission date |
Jan 24, 2023 |
| Last update date |
Jan 29, 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 |
| |
|
| Platform ID |
GPL24995 |
| Series (1) |
| GSE223636 |
Differential Nodal level promotes mesendoderm cell fate segregation mediated by chromatin organization |
|
| Relations |
| BioSample |
SAMN32896487 |
| SRA |
SRX19158409 |
