|
| Status |
Public on Dec 22, 2022 |
| Title |
zebrafish wild-type explant 10hpf |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish cells
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB
tissue: embryonic cells
age: 10hpf
genotype: wild type
|
| Treatment protocol |
phenol red 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 10hpf(corresponding to embryonic developmental stage) separately.
|
| 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) 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 3.0.2) with default parameters.
Assembly: GRCz11
Supplementary files format and content: tar compressed files included filtered_gene_bc_matrices after running CellRanger pipeline
|
| |
|
| Submission date |
Dec 17, 2022 |
| Last update date |
Dec 22, 2022 |
| 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) |
| GSE221220 |
Nodal coordinates the anterior-posterior patterning of germ layers and induces head formation in zebrafish explants. |
|
| Relations |
| BioSample |
SAMN32298616 |
| SRA |
SRX18756814 |
