Home-Dog10K database

The goal of Dog10K project is to coordinate global efforts in canine genome sequencing and to build a comprehensive resource for the dog community. We have developed the Dog10K database to provide a platform for users to browse, search, analyse and download Dog10K data. We are also dedicated to providing a broad and multidimensional collection of canine multi-omics data, providing visualisation, analysis and download of multi-omics data. Up to now, the Dog10k database has included SNP information from 2,075 canine individuals, de-novo mutation (DNM) data from 404 trios, single-cell RNA sequencing (scRNA-seq) data from the hippocampus of 1 dog brain and the leukocytes from 17 dogs, and transcriptomic data from 30 dogs of different ages. We've also integrated some analysis tools such as Genome Browser, Liftover, Selscan and Age Conversion.[more]

This database was published in Nucleic Acids Research on October 22, 2024. (https://doi.org/10.1093/nar/gkae928)

Summary

Statistics

SNVs

The 2,075 samples collected for Dog10K were selected to represent a wide variety of breeds of differing morphology, history, and behavior. Primary SNV and small indel variant discovery was performed on 1,987 samples fulfilling initial quality threshold.[more]

DNMs

The authors identified 8,312 high-quality DNMs from 643 dogs (341 females, 302 males) of 54 multigenerational families from 404 trios representing 43 distinct dog breeds, with an average of 21.31 DNMs per trio. [more]

scRNA

Hippocampus: The authors obtained scRNA-seq data of the hippocampus of 5-month-old Beagle dogs using SPLiT-seq. They created a digital expression matrix of 105,057 single nuclei with a median of 804 genes and 1,109 counts per nucleus. Based on the differentially expressed genes (DEGs) in each cell cluster, we identified 8 cell types. [more]

Leukocytes: The authors isolated circulating leukocytes from 6 male and 4 female middle-aged tumor bearing dogs diagnosed with osteosarcoma. The cells obtained from the cancer burdened dogs were integrated with the 7 healthy samples to obtain a complete dataset of 74,067 cells. They identified 46 unique clusters with the major immune cell types. [more]

Aging transcriptome

RNA-seq data were obtained from 30 dogs of different ages from 1 to 9 years, aligned to the reference genome, and gene expression was calculated. The whole blood expression data of 469 healthy people at different ages from 8 to 73 years were downloaded from the GSA database (https://ngdc.cncb.ac.cn/gsa/) of National Genomics Data Center (NGDC). [more]