Table 1.
Multi-organ and organ-specific endothelial cell scRNA-seq and multiome atlases
| Organ system | Species | Developmental stage | Dataset contents | Single-cell capture and scRNA-seq method | Refs. |
|---|---|---|---|---|---|
| Multi-organ | Mouse | Adult | scRNA-seq | Smart-seq2 and 10× Genomics 3′ | 95 |
| scRNA-seq | Microwell-seq | 73 | |||
| scRNA-seq | Smart-seq2 | 74 | |||
| scRNA-seq, RNA-seq, ATAC-seq, MethylC-seq | 10× Genomics GemCode | 33 | |||
| sci-ATAC-seq | sci-ATAC-seq | 75 | |||
| Human | Embryonic (E72–E129) | sci-RNA-seq, sci-ATAC-seq | sci-RNA-seq3 | 76,92 | |
| Adult (22–74 years) | scRNA-seq | Smart-seq2 and 10× Genomics 3′ | 93 | ||
| Heart | Mouse | Embryonic (E12.5–E14.5) | scRNA-seq | 10× Genomics 3′ | 29 |
| Mouse, human | Embryonic mouse (E12, E17.5), embryonic human (11 weeks, 14 weeks, 22 weeks), adult mouse | scRNA-seq | 10× Genomics 3′ | 66 | |
| Human | Embryonic (5–25 weeks) | scRNA-seq | STRT-seq | 77 | |
| Adult (40–75 years) | scRNA-seq | 10× Genomics 3′ | 78 | ||
| Lung | Mouse | Embryonic (E12.5–E17.5), postnatal (P3–P42) | scRNA-seq, scATAC-seq | 10× Genomics 3′ | 79 |
| Postnatal (P1) | scRNA-seq | Drop-seq | 80 | ||
| Postnatal (P3, P7, P14) | scRNA-seq | MULTI-seq | 81 | ||
| Human | Adult | scRNA-seq | Smart-seq2 and 10× Genomics 3′ | 82 | |
| Adult | scRNA-seq | 10× Genomics 3′ | 83 | ||
| Brain | Mouse | Embryonic (E14.5) | RNA-seq (TRAP-seq), scRNA-seq | TruSeq v2 | 84 |
| Adult | scRNA-seq | Smart-seq2 | 65 | ||
| Mouse, human | Adult mouse, paediatric and adult human | snRNA-seq | 10× Genomics 3′ | 67 | |
| Human | Fetal, adult | scRNA-seq | 10× Genomics 3′ | 69 | |
| Adult | scRNA-seq, RNA-seq | 10× Genomics 3′ | 68 | ||
| Kidney | Mouse | Embryonic | scRNA-seq | 10× Genomics 3′ | 85 |
| Embryonic E14.5 | scRNA-seq | 10× Genomics 3′ | 87 | ||
| Embryonic E14.5 | scRNA-seq | Drop-seq, Chromium 10× Genomics and Fluidigm C1 | 86 | ||
| Embryonic, adult | snRNA-seq, sn-ATAC-seq | Smart-seq2 and 10× Genomics 3′ | 88 | ||
| Human | Embryonic, paediatric, adult | scRNA-seq | 10× Genomics 3′ | 89 | |
| Embryonic (12–18 weeks) | scRNA-seq | Drop-seq | 90 | ||
| Embryonic (9–19 weeks) | scRNA-seq | 10× Genomics 3′ | 91 | ||
| Adult | snRNA-seq, sn-ATAC-seq | 10× Genomics 3′ v2 | 96 | ||
| Liver | Mouse | Embryonic (E12–E18), postnatal (P2–P30) | scRNA-seq, bulk RNA-seq | 10× Genomics 3′ | 97 |
| Adult | scRNA-seq | MARS-seq | 98 | ||
| scRNA-seq | 10× Genomics 3′ | 99 | |||
| Human | Adult | scRNA-seq | CEL-seq2 | 100 | |
| scRNA-seq | 10× Genomics 3′ | 101 |
ATAC-seq, assay for transposase-accessible chromatin using sequencing; CEL-seq2, cell expression by linear amplification and sequencing; Drop-seq, droplet sequencing; E, embryonic day; MARS-seq, massively parallel RNA single-cell sequencing; MULTI-seq, multiplexing using lipid-tagged indices for single-cell and single-nucleus RNA sequencing; P, postnatal day; scRNA-seq, single-cell RNA sequencing; snRNA-seq, single-nucleus RNA sequencing; sci-ATAC-seq, single-cell combinatorial indexing assay for transposase-accessible chromatin using sequencing; sci-RNA-seq, single-cell combinatorial indexing RNA sequencing; Smart-seq2, switching mechanism at the 5′ end of the RNA template sequencing; sn-ATAC-seq, single-nucleus combinatorial indexing assay for transposase-accessible chromatin using sequencing; STRT-seq, single-cell tagged reverse transcription sequencing; TRAP-seq, targeted purification of polysomal mRNA.