|
| Status |
Public on Dec 10, 2023 |
| Title |
WT_KM_1 |
| Sample type |
SRA |
| |
|
| Source name |
renal cells
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB strain
tissue: Kidney
genotype: wild type
transgene: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For scRNA-Seq analysis of eosinophils from kidney, eosinophils were sorted from adult Tg(eslec:eGFP) kidneys. For scRNA-Seq analysis of renal cells of different genotypes, kidneys were collected from WT, cebp1-/-, and cebpb-/- individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x 3' scRNA-Seq GEM generation.
Post GEM generation, the library construction was performed strictly based on the manufacturer’s instructions (10x Genomics, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Post basecalling, the fastq files were mapped to the zebrafish genome with the CellRanger package.
Output files of CellRanger were applied to the R package "Seurat".
Samples were filtered to remove low quality or contaminated cells.
The renal cells from different genotypes (sample 1-9) were integrated with the "IntegrateData" function of Seurat.
Further analyses was performed based on the instructions of "Seurat" package.
Assembly: GRCz11
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell, cell and gene metadata for integrated KM cells and KM eosinophils, and the relevant Seurat objects (rds files).
|
| |
|
| Submission date |
Oct 23, 2023 |
| Last update date |
Dec 11, 2023 |
| Contact name |
Gaofei Li |
| E-mail(s) |
15013156757@126.com
|
| Organization name |
South China University of Technology
|
| Street address |
Guangzhou Higher Education Mega Centre, Panyu District
|
| City |
Guangzhou |
| ZIP/Postal code |
510006 |
| Country |
China |
| |
|
| Platform ID |
GPL24995 |
| Series (2) |
| GSE198314 |
Cebp1 and Cebpβ transcriptional axis controls eosinophilopoiesis in zebrafish |
| GSE246039 |
Cebp1 and Cebpβ transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA-Seq] |
|
| Relations |
| BioSample |
SAMN37930601 |
| SRA |
SRX22195223 |
