|
| Status |
Public on Dec 01, 2023 |
| Title |
Wild-type |
| Sample type |
SRA |
| |
|
| Source name |
Whole heart
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Whole heart
cell type: Heart cells
genotype: tnnt2a+/+
developmental stage: 72 hpf
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 10000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10xGenomics).
Library preparation was conducted according to the manufacturer indications.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Sequencing was done on Nextseq2000 and raw reads were aligned against the zebrafish genome (DanRer11) and counted by StarSolo
Preprocessed counts were further analysed using Scanpy ollowed by secondary analysis in Annotated Data Format.
Preprocessed counts were further analyzed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 117 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 40%. Furthermore, we filtered 9060 genes if they were detected in less than 30 cells (<0.01%).
Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance. We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding (McInnes & Healy, https://arxiv.org/abs/1802.03426) and cell clustering via community detection, 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 |
May 18, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Stefan Günther |
| E-mail(s) |
stefan.guenther@mpi-bn.mpg.de
|
| Organization name |
MPI for heart and lung research
|
| Street address |
ludwigtr. 43
|
| City |
bad nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30614 |
| Series (1) |
| GSE232835 |
Gene expression profile at single cell level of 72 hpf heart cells from wild-type, tnnt2a mutant, and Tnnt2a degron zebrafish larvae. |
|
| Relations |
| BioSample |
SAMN35166242 |
| SRA |
SRX20432556 |
