OVERVIEW


FishSCT is a fish single-cell transcriptome database, with Danio rerio as the primary study subject. We collected 129 datasets from 44 projects from GEO and SRA common platforms and conducted unified analysis through a pipeline.

Finally, 964 / 26,965 marker / potential marker gene information of 245 cell type and a large number of expression profiles with single cell resolution were obtained. Among them, Danio rerio datasets are up to 117, covering 25 tissues at 36 time points in the growth and development stage of Danio rerio. In addition to Danio rerio, we also included the scRNA-seq data of 8 fish species to enable users to conduct comparative analysis between species.

Cite: Cheng Guo, Weidong Ye, Mijuan Shi et al. FishSCT: a zebrafish-centric database for exploration and visualization of fish single-cell transcriptome. Science China Life Science (2023). 10.1007/s11427-022-2293-4.




RELATED SPECIES

FishSCT covers 9 species, which are classified into model, economic, ornamental and ecological fish according to several article introduction.

DATA SOURCE

We collected 129 datasets from 44 projects from GEO and SRA published before October 2022. Among them, Danio rerio datasets are up to 117.

EXPERIMENT TYPE

We manually classified 129 datasets according to experiment types (eg: baseline: 83 datasets). And we organized the relevant information of 45 articles.

TISSUE

The datasets in FishSCT cover 30 tissue types. Among them, Danio rerio datasets cover 25 tissue types at 36 time points in the growth and development stage of Danio rerio.

CELL TYPE

FishSCT stored marker information and expression profile data for 245 cell types. Users can get friendly visualization services on the page.

MARKER ANNOTATION

Information of 964 / 26,965 markers / potential markers is available on the page and is available for free download.


STATISTICS OF SPECIES

FishSCT stored 848 / 13,800 marker / potential marker information for 222 cell types of Danio rerio, and it's datasets cover 25 tissue types at 36 time points in the growth and development stage. The statistics of cell types and markers in each tissue are shown in the figure below left.

The figure on the below right is a drill-down pie chart, showing the marker proportion information of tissue and cell types of Danio rerio. When users click on the sector area, the figure will be switched to the next level to show the marker proportion of cell types contained in the tissue.


The phylogenetic relationships among the ray-finned fishes in FishSCT are shown in the figure below left. In addition to Danio rerio, Oryzias latipes is also the model species. FishSCT also includes scRNA-seq data for several economically important fish species.

FishSCT stored 116 / 13,165 marker / potential marker information for 59 cell types of other 8 fishes. The statistics of cell types and markers in each fish are shown in the following figure on the right.


BASIC INFORMATION OF SPECIES


 Danio rerio

Genome version:
GRCz11
Transcriptome source:
ensembl

 Astyanax mexicanus

Genome version:
Astyanax_mexicanus-2.0
Transcriptome source:
NCBI(RefSeq assembly)

Tissue: hypothalamus
Experiment type: baseline
Source dataset id:
SRR11886701, SRR11917464, SRR15422711, SRR15422691, SRR15422671, SRR15422704, SRR15422680, SRR15422698, SRR15422699, SRR15422703

 Gasterosteus aculeatus

Genome version:
GAculeatus_UGA_version5
Transcriptome source:
ensembl

Tissue:
 > embryo
Experiment type:
 > baseline
Source dataset id:
 > SRR17665713

 Nothobranchius furzeri

Genome version:
Nfu_20140520
Transcriptome source:
NCBI(RefSeq assembly)

Tissue:
 > caudal fin
Experiment type:
 > regeneration
Source dataset id:
 > SRR11886701, SRR11917464

 Oryzias latipes

Genome version:
ASM223467v1
Transcriptome source:
ensembl

Tissue:
 > pituitary
Experiment type:
 > baseline
Source dataset id:
 > GSM4959937, GSM4959938

 Oreochromis niloticus

Genome version:
O_niloticus_UMD_NMBU
Transcriptome source:
NCBI(RefSeq assembly)

Tissue:
 > anterior kidney
Experiment type:
 > baseline
Source dataset id:
 > SRR16095434

 Monopterus albus

Genome version:
M_albus_1.0
Transcriptome source:
ensembl

Tissue:
 > gonad
Experiment type:
 > baseline
Source dataset id:
 > GSM4661001

 Mastacembelus armatus

Genome version:
fMasArm1.2
Transcriptome source:
NCBI(RefSeq assembly)

Tissue:
 > ovotestes
Experiment type:
 > baseline
Source dataset id:
 > GSM5333024

 Oncorhynchus mykiss

Genome version:
USDA_OmykA_1.1
Transcriptome source:
ensembl

Tissue:
 > blood
Experiment type:
 > baseline
Source dataset id:
 > GSM4792223, GSM4792224, GSM4792225


 DATA SOURCES