|
| Status |
Public on Mar 25, 2024 |
| Title |
WT, replicate 1, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
whole zebrafish embryo
|
| Organism |
Danio rerio |
| Characteristics |
cell type: Kdrl positive
tissue: whole zebrafish embryo
strain: Tg(kdrl:EGFP)zf531Tg
age: 3dpf
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Zebrafish embryos (3dpf) were anesthethised with Tricain. Embryos were dissociated using a mix of 0.25% Trypsin and collagenase (4mg/mL), centrifuged to collect the cells, resuspended into DMEM + 10% Fetal Bovine Serum and filtered to remove the debris. Alive cells were then FACS sorted for GFP+ cells and using non transgenic animals as control. Cells were washed and resuspend in PBS prior 10X genomic experiment
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCZ11 v107
Supplementary files format and content: matrix files
|
| |
|
| Submission date |
Mar 20, 2023 |
| Last update date |
Mar 25, 2024 |
| Contact name |
Laetitia Preau |
| E-mail(s) |
laetitia.preau@kit.edu
|
| Organization name |
Karlsruhe Institute of Technology (KIT)
|
| Street address |
Fritz Haber Weg 4
|
| City |
Karlsruhe |
| ZIP/Postal code |
76131 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30614 |
| Series (2) |
| GSE227696 |
Gene expression profile at single cell level of kdrl+ FACS sorted cells from WT or flt1 mutant Tg(kdrl:EGFP) zebrafish embryos (3dpf). |
| GSE227807 |
Gene expression profile at single cell level of WT or flt1 mutant |
|
| Relations |
| BioSample |
SAMN33830063 |
| SRA |
SRX19731086 |
