scRNA-seq & snRNAseq dataset
Integrated atlas objects (Seurat, .rds) can be downloaded directly from this site:
| Integrated atlas | Species | Size | Download |
|---|---|---|---|
| Cross-model integrated atlas | Mouse | 23.8 GB | scPKD_mouse_integrated_atlas.rds |
| Integrated atlas, non-immune compartment | Human | 1.7 GB | scPKD_human_nonimmune_atlas.rds |
| Integrated atlas, immune compartment | Human | 493 MB | scPKD_human_immune_atlas.rds |
IMPORTANT: If you are unable to download, please try to right click the ‘download’ link and select ‘save link as’. All downloads support resuming, so large files can also be fetched with wget -c <url> or curl -C - -O <url>.
Raw sequencing data for each individual sample are available from NCBI GEO under the accession numbers listed in the table below.
| scPKD ID | GSE ID | Species | Disease | Sex | Age |
|---|---|---|---|---|---|
| PKD00101 | GSM5627690 | Human | Healthy | M | 54 |
| PKD00102 | GSM5627691 | Human | Healthy | M | 62 |
| PKD00103 | GSM5627692 | Human | Healthy | F | 61 |
| PKD00104 | GSM5627693 | Human | Healthy | M | 50 |
| PKD00105 | GSM5627694 | Human | Healthy | F | 52 |
| PKD00106 | GSM5627695 | Human | PKD | F | 50-60 |
| PKD00107 | GSM5627696 | Human | PKD | F | 50-60 |
| PKD00108 | GSM5627697 | Human | PKD | F | 50-60 |
| PKD00109 | GSM5627698 | Human | PKD | M | 50-60 |
| PKD00110 | GSM5627699 | Human | PKD | F | 60-70 |
| PKD00111 | GSM5627700 | Human | PKD | M | 30-40 |
| PKD00112 | GSM5627701 | Human | PKD | M | 40-50 |
| PKD00113 | GSM5627702 | Human | PKD | M | 40-50 |
| PKD00201 | GSM8291973 | Mouse | Healthy | M | D66 |
| PKD00202 | GSM8291976 | Mouse | Healthy | M | D66 |
| PKD00203 | GSM8291977 | Mouse | Healthy | M | D100 |
| PKD00204 | GSM8291979 | Mouse | Healthy | M | D100 |
| PKD00205 | GSM8291981 | Mouse | Healthy | M | D100 |
| PKD00206 | GSM8291986 | Mouse | Healthy | M | D130 |
| PKD00207 | GSM8291987 | Mouse | Healthy | M | D130 |
| PKD00208 | GSM8291988 | Mouse | Healthy | M | D130 |
| PKD00209 | GSM8291974 | Mouse | PKD | M | D66 |
| PKD00210 | GSM8291975 | Mouse | PKD | M | D66 |
| PKD00211 | GSM8291978 | Mouse | PKD | M | D100 |
| PKD00212 | GSM8291980 | Mouse | PKD | M | D100 |
| PKD00213 | GSM8291982 | Mouse | PKD | M | D100 |
| PKD00214 | GSM8291983 | Mouse | PKD | M | D130 |
| PKD00215 | GSM8291984 | Mouse | PKD | M | D130 |
| PKD00216 | GSM8291985 | Mouse | PKD | M | D130 |
Source code
- Front-end: https://github.com/OSU-BMBL/pkd-database
- Back-end: https://github.com/OSU-BMBL/pkd-database-backend
- STAR Protocols: https://github.com/OSU-BMBL/ssread-protocol