Table 1.
Mouse spermatogenesis single-cell RNA-seq datasets.
| Chen Y et al. (2018), Cell Res | Ernst C et al. (2019). Nat Commun | Green CD et al (2018), Dev Cell | Grive JK et al. (2019), PLoS Genet | Han X et al. (2018), Cell | Hermann BP et al. (2018), Cell Rep | Jung M et al. (2018), BioRxiv | La HM et al. (2018), Nat Commun | Liao J et al. (2019), Development | Makino Y et al. (2019). Sci Rep | Neirijunck et al. (2018), Endocrinology | Lukassen S et al. (2018), Sci Rep | Song HW et al. (2016). Cell Rep | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total cell number | 1204 | 53 510 (from 2 P5, 1 P10, 1 P15, 1 P20, 1 P25, 1 P30, 1 P35, 2 8–9 week mice) | 34 633 | 1200–2500 per sample (from 1 P6, 1 P14, 1 P18, 1 P25, 1 P30, 1 8week mice) | 19 659 (>50 mice) | 31 163 (from 21 adult mice, 30 P6 mice) | 62 600 (from 11 to 38 week WT, Mlh3 KO, Cul4a KO, Hormad1 KO, and Cnp mice) | Not mentioned | 71 | 175 (80 from P1.5, 48 from P3.5, and 47 from P5.5) | Interstitial steroidogenic progenitor cells (6362 cells), SCs (1932 cells), fetal Leydig cells (521 cells), primordial germ cells (483 cells), and endothelial cells (180 cells) from E16.5 | 2500 (1250 each from 2 mice) | 181 (71 from P3 WT, 53 from P7 WT, 57 from Rhox10 KO P3) |
| First-Wave | + | + | – | + | – | + | – | – | + | + | – | – | + |
| Unselected steady-state spermtogenesis | – | + | + | + | – | + | + | – | – | – | – | + | – |
| Sorted Spermatogonia | + | – | + | + | – | + | + | + | – | – | – | – | – |
| Sorted Spermatocytes | + | – | + | + | – | + | + | – | – | – | – | – | – |
| Sorted Spermatids | + | – | + | + | – | + | + | – | – | – | – | – | – |
| Somatic cells | – | Sertoli cells, Leydig cells, Myoid cells, Endothelial cells, Marcrophages | Sertoli cells, Leydig cells, Myoid cells, Endothelial cells, Macrophage, Inntate Lymphosid | Sertoli cells, Endothelial, Hematopoietic cells, Smooth muscle | – | Sertoli cells, Peritubular cells (adult) | Sertoli cells, Leydig cells | – | – | Sertoli cells | Endothelial cells, fetal Leydig cells, Sertoli cells | Sertoli cells, Leydig cells | – |
| Validation methods | Knockout, ChIP-seq | RNA scope, ChIP-seq | IHC, smFISH | IHC | – | IHC, qRT-PCR | Knockout, IHC | Knockout, Transplantation, Bulk RNA-seq, IHC | IHC, Function (RA inhibitior) | Knockout, ChIP-qPCR, IHC, WB | Knockout in Sertoli cells | – | Knockout, IHC |
| scRNA-seq Chemistry/Method | 3′ sequencing and full length sequence (SMART-seq2) | 3′ sequencing and barcoding (10x Genomics) | 3′ sequencing and barcoding (Oliginal Drop-seq) | 3′ sequencing and barcoding (10x Genomics) | 3′ sequencing and barcoding (SMART-seq2 and Microwell-seq) | full length sequence (Fluidigm C1), 3′ sequencing and barcoding (10x Genomics) | 3′ sequencing and barcoding (10x Genomics) | 3′ sequencing and barcoding (10x Genomics) | full length sequence (Fluidigm C1) | full length sequence (Fluidigm C1) | 3′ sequencing and barcoding (10x Genomics) | 3′ sequencing and barcoding (10x Genomics) | full length sequence (Fluidigm C1) |
| Replication | Replication unclear | 1 replicate (P10, P15, P20, P25, P30, and P35) and 2 biological replicates (P5 and adult) | 6 x samples from individual adult mice. | 1 replicate | 2 replicates of adult testes | 5 x C1 P6 ID4-EGFP, 4 x C1 adult ID4-EGFP, 1 x 10x Genomics P6 ID4-EGFPbright, 1 x 10x Genomics P6 ID4-EGFPdim, 1 x 10x Genomics P6 unselected testis cells, 1 x 10x Genomics Adult ID4-EGFPbright, 1 x 10x Genomics Adult ID4-EGFPdim, 1 x 10x Genomics Adult unselected testis cells, 3 x 10x Genomics adult steady-state spermatogenesis (unselected), 1 x Adult StaPut Spermatocytes, 1 x Adult StaPut Round Spermatids | 11 x Unselected testis cells from adult mice, 1 x spermatogonia, 1 x primary spermatocytes, 1 x secondary spermatocytes, 1 x Spermatids | 2 x biolgical replicates, each from one mouse | 1 replicate | 1 replicate | 2 x E16.5 testes | 2 biological replicates | 2 replicates of ID4-positive testicular cells from Wildtype at P3 and P7, 3 replicates of Rhox10 knockout mice at P3 |
| GEO number | GSE107644 | E-MTAB-6946 | GSE112393 | GSE121904 | GSE108097 | GSE108970, GSE108974, GSE108977, GSE109049, GSE109033, and GSE109037 | GSE113293 | GSE112880 | GSE107711 | PRJNA524391 | GSE123119 | GSE104556 | GSE82174 |