|
| Status |
Public on Feb 13, 2024 |
| Title |
80hpf |
| Sample type |
SRA |
| |
|
| Source name |
heart
|
| Organism |
Danio rerio |
| Characteristics |
tissue: heart
genotype: wild type
age: 80hpf
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without Calcium and Magnesium and with 0.04% BSA.
Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3สน Reagent Kits v3,1 (10xGenomics). scRNA-seq library preparation was done using a standard protocol, and sequencing was done on a Nextseq2000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Reads were aligned against the zebrafish genome and counted by StarSolo.
Preprocessed counts were further analysed using Scanpy.
Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed cells that did not express more than 300 genes or had a mitochondrial content greater than 8%. Furthermore, we filtered genes if they were detected in less than 30 cells.
Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding and cell clustering, were based on the initial PCA.
Final data visualization was done by scanpy and cellxgene packages.
Assembly: DanRer11
Supplementary files format and content: starsolo outputs
|
| |
|
| Submission date |
Sep 06, 2023 |
| Last update date |
Feb 13, 2024 |
| Contact name |
Noah Knoppik |
| Organization name |
Max-Planck-Institute for Heart and Lung Research
|
| Department |
Bioinformatics
|
| Street address |
Ludwigstrasse 43
|
| City |
Bad Nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30614 |
| Series (1) |
| GSE242483 |
scRNA-seq of 50 and 80 hpf isolated zebrafish hearts |
|
| Relations |
| BioSample |
SAMN37304285 |
| SRA |
SRX21649989 |
