|
| Status |
Public on Jan 28, 2021 |
| Title |
zebrafish Nodal explants 8hpf |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish cells
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB
tissue: embryonic cells
age: 8hpf
treatment: injected with 10pg ndr2 mRNA
|
| 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 4hpf, 5hpf, 6hpf, 8hpf, 10hpf and 24hpf (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 v2 (10x Genomics, PN-120237) according to the manufacturer’s protocol for 10000 cells recovery.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina sequencing reads were aligned to the zebrafish mRNA reference genome (GRCz11 or GRCz10) using the 10x Genomics CellRanger pipeline (version 2.1.1) with default parameters.
Genome_build: GRCz11/GRCz10
Supplementary_files_format_and_content: tar compressed files included filtered_gene_bc_matrices after running CellRanger pipeline
|
| |
|
| Submission date |
Jan 27, 2021 |
| Last update date |
Jan 29, 2021 |
| 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 (2) |
| GSE165653 |
Single cell response landscape of graded Nodal signaling in zebrafish explants [single-cell RNA-seq] |
| GSE165654 |
Single cell response landscape of graded Nodal signaling in zebrafish explants |
|
| Relations |
| BioSample |
SAMN17609987 |
| SRA |
SRX9963430 |
