Table 2.
Clusters (or cell types) discovered in the reduced subspace and their associated markers
| Cluster ID | Label | Markers |
|---|---|---|
| 0 | Unclustered | |
| 1 | Primitive erythrocyte progenitor (Baron, 2013) | Hba-x (Leder et al., 1992), Hbb-bh1 (Kingsley et al., 2006), Gata1 (Baron, 2013), Lmo2 (Palis, 2014) |
| 2 | Mesoderm | Car3, Spag5, Hoxb1 (Carapuço et al., 2005), Cnksr3, Smad4, Zfp280d, Vim (Saykali et al., 2019), Ifitm1 |
| 3, 4 | Lateral plate mesoderm | Foxf1 (Mahlapuu et al., 2001), Hand1 (Riley et al., 1998) |
| 5 | Anterior visceral endoderm | Sox17, Foxa2 (Perea-Gomez et al., 2001), Cer1 (Torres-Padilla et al., 2007), Frat2, Lhx1 (Costello et al., 2015), Hhex (Norris et al., 2002), Gata6, Ovol2, Otx2 (Perea-Gomez et al., 2001), Sfrp1 (Pfister et al., 2007) |
| 6,7 | Extraembryonic mesoderm | Fgf3 (Niswander and Martin, 1992), Lmo2 (Palis, 2014), Gata2 (Silver and Palis, 1997), Bmp4 (Fujiwara et al., 2001) |
| 8,9 | Visceral endoderm 1 | Rhox5 (Lin et al., 1994), Emb (Shimono and Behringer, 1999), Afp (Kwon et al., 2006) |
| 10,11 | Neuromesodermal progenitor | Sox2, T (Koch et al., 2017) |
| 12,13 | Paraxial mesoderm/presomitic mesoderm | Hoxa1, Hoxb1 (Carapuço et al., 2005), Cdx1, Cdx2 (van den Akker et al., 2002) |
| 14 | Posterior primitive streak | Mesp1 (Arnold and Robertson, 2009), Snai1 (Smith et al., 1992), Lhx1 (Costello et al., 2015; Shawlot et al., 1999), Smad1 (Tremblay et al., 2001) |
| 15 | Anterior primitive streak, organizer-like cells | Foxa2 (Arnold et al., 2008), Gsc (Lewis et al., 2007), Eomes (Arnold et al., 2008) |
| 16,17 | Posterior primitive streak derived mesoderm, lateral plate mesoderm progenitors | Msx2 (Catron et al., 1996), Snai1 (Smith et al., 1992), Foxf1 (Mahlapuu et al., 2001), Hand1 (Riley et al., 1998), Gata4 (Simon et al., 2018) |
| 18,19 | Extraembryonic ectoderm | Cdx2 (Beck et al., 1995), Rhox5 (Lin et al., 1994), Id2 (Jen et al., 1997), Gjb5 (Frankenberg et al., 2007), Tfap2c (Latos et al., 2015), Zfp42(aka Rex1) (Pelton et al., 2002), Elf5 (Latos et al., 2015), Gjb3 (Frankenberg et al., 2007), Ets2 (Donnison et al., 2015) |
| 20 | Ectoplacental cone | Plac1 (Donnison et al., 2015), Ascl2 (Simmons and Cross, 2005) |
| 21 | Definitive endoderm | Sox17 (Viotti et al., 2014), Foxa2 (Burtscher and Lickert, 2009), Apela (Hassan et al., 2010) |
| 22 | Mesendo progenitor, primitive streak | Tcf15 (Chal et al., 2018), Cer1, Hhex (Thomas et al., 1998) |
| 23 | Posterior primitive streak, cardiac mesoderm progenitors | Mesp1 (Arnold and Robertson, 2009), Gata4 (Simon et al., 2018), Lhx1 (Shawlot et al., 1999), Smad1 (Tremblay et al., 2001) |
| 24,25 | Primitive streak | T, Mixl1, Eomes, Fgf8, Wnt3 |
| 26 | Klf10, Gpbp1l1, Hmg20a, Rbm15b, Celf2 | |
| 27-28 | Posterior-proximal epiblast | Nanog (Mulas et al., 2018), Sox2 (Avilion, 2003), Pou5f1 (Mulas et al., 2018), Otx2 (Kurokawa et al., 2004) |
| 29-34 | Epiblast | Sox2 (Avilion, 2003), Pou5f1 (Mulas et al., 2018), Otx2 (Kurokawa et al., 2004) |