|
Status |
Public on Dec 10, 2023 |
Title |
KM_eos |
Sample type |
SRA |
|
|
Source name |
eosinophils
|
Organism |
Danio rerio |
Characteristics |
strain: AB strain tissue: Kidney genotype: wild type transgene: Tg(eslec:eGFP)
|
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).
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|
|
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).
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|
|
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 |
SAMN37930592 |
SRA |
SRX22195232 |