Table 1. Unique gene signatures of the 14 different cell types (clusters) from the developing rat uteri on PND 6.
Gene markers revealed by single cell RNA sequencing, sorted by highest adjusted p-value with positive LogFc (Figure 3—source data 1). Clusters identities were assigned to different cell types by RNAish validation and/or manual literature review. Top 15 markers, citations, and associations are listed in the table. Selected markers were further validated in Figure 3.
| Outer stroma (1) |
Myometrium (2) |
Inner stroma (3) |
Inhibited Progenitor (4) |
Epithelium (5) |
Proliferating cells (6) |
Vascular endothelium (7) |
Dividing epithelium (8) |
Mesothelium (9) |
Myeloid (10) |
Erythroid (11) |
Pericyte (12) |
Lymphatic endothelium (13) |
Neuronal (14) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RGD1305645 | Lum | Nrgn | AC109891.2 | Cd24 ** | Hmgb2 | Cd93 * |
Epcam *
(Litvinov et al., 1997) |
Bsg | Fcer1g * | Hba.a1 * | Mgp * | Ccl21 | Plp1 * |
|
Smoc2 *
(Mucenski et al., 2019) |
Postn | Cpxm2 ** |
Rn60_1_221
6.1 |
Epcam *
(Litvinov et al., 1997) |
Stmn1 * |
Cdh5 **
(Bhasin et al., 2010) |
Cldn3 | Upk1b * | Tyrobp * | Hba.a2 * |
Mcam **
(Barron et al., 2016) |
Mmrn1 ** |
Sox10 *
(Nonaka et al., 2008) |
| Dpt * |
NEWGENE_
621351 |
Tgfbi * |
AABR070687
05.1 |
Wfdc2 *
(Mucenski et al., 2019) |
Top2a *
(Whitfield et al., 2006) |
RGD1310587 | Cd24 * |
Msln **
(Chang and Pastan, 1996) |
Csf1r **
(MacDonald et al., 2010) |
LOC1036948
57 |
Rergl * |
Lyve1**
(Hirakawa et al., 2003) |
Gfra3 * |
| Cpe | Col1a1 | Plac8 | Fgfr2 |
Wnt7a *
(Miller and Sassoon, 1998) |
Mki67 *
(Whitfield et al., 2006) |
Emcn * | Cdh1 * | Fmod | Lyz2 * | Hbb * | Eln * |
Flt4 **
(Hirakawa et al., 2003) |
Abca8a |
| Vcan * |
Ptn *
(Mucenski et al., 2019) |
Vcan * |
Unc5b *
(Mullen et al., 2018) |
Cldn3 | Tubb5 * | Tie1 * | Klf5 | Cav1 | Ftl1 |
LOC1036948
55 |
Col4a1 * | Cldn5 * | Egfl8 |
| Dcn * | Thbs2 ** | Fn1 * | Ugt1a2 | Krt8 * |
LOC1003595
39 |
Plvap | Krt8 * | Dpp4 * | Cybb * |
Alas2 *
(Kaneko et al., 2014) |
Igfbp7 * | Fgl2 * | Cdh19 |
| Col4a5 * | Col3a1 | Apcdd1 |
Bambi **
(Mullen et al., 2018) |
Cdh1 * | Racgap1 | Cav1 | Mt1 | Anxa3 | Laptm5 * | Ybx3 * | Cspg4 ** | Klhl4 * | Afap1l2 |
| Apoe |
Ogn
(Mucenski et al., 2019) |
Cdh11 * | Srgn | Tacstd2 |
LOC1003603
16 |
Adgrl4 |
Wnt7a *
(Miller and Sassoon, 1998) |
Igfbp6 | Tmsb4x | Hba.a3 * | Abcc9 * | Cdh5 * | L1cam * |
| Osr2 | Sparc | Col6a3 * | Kcnk3 | Cldn4 * | Prc1 * | Plxnd1 | Mt2A | Cfb | Ctsb * | Alox15 | Epas1 | Tbx1 | Col5a3 |
| Tnfrsf21 | Cxcl12 | Tnfrsf21 | Igfbp5 | Msx1 | Cdk1 * | Epas1 * | Msx1 | Lox | Lcp1 * | Car2 | Rgs5 | Slc45a3 | Olfml2a |
| Adamts7 | Igfbp5 | Nkd2 | Igf2r | Klf5 | Depdc1 | Esam * | Wfdc2 | Muc16 * | Ptprc * | Ahsp * | Foxs1 * | Adgrg3 | Metrn |
| Slc26a7 | Ccdc80 | Axin2 | Plac8 | Elf3 * | Smc2 | Cyyr1 | Dlx5 | Itm2a | C1qa * | Rbm38 | Myl9 | Sdpr | Mpz * |
| Wfikkn2 ** | Gpc3 | Vim * | Prrx2 | Dlx5 | Kif11 * | Clec14a | Sbspon | Sema3c | C1qc * | Lgals5 | RGD1564664 |
LOC1009120
34 |
Plekha4 |
| Col6a3 * | Igsf10 | Col6a2 * | Alpl | Aldh2 | Cenpf * | Adgrf5 |
Hmgb2 **
(Stros et al., 2009) |
Fbln2 * | Aif1 * | Slc4a1 | Acta2 * |
Rn50_1_043
5.2 |
Dbi |
| Islr | Itm2a * |
AABR070253
16.1 |
Mt2 | Tmpo * | Col3a1 | Tacstd2 | Eln | Cxcl2 | Slc25a39 | Cald1 * | Il2rg | Col20a1 | |
| * extracellular matrix, collagen or cytoskeleton related **validated new marker (in uterus) |
* muscle related **validated new marker (in uterus) | *extracellular matrix, collagen or cytoskeleton related **validated new marker (in uterus) |
*implicated during Mullerian duct regression in males ** validated new marker (in uterus) | *epithelium associated **validated new marker (in uterus) | *cell cycle or proliferation associated | *endothelial related **implicated higher expression in vascular tissues | *epithelium associated **cell proliferation associated |
*mesothelium associated or enriched **mesothelium specific | * myeloid associated (Zilionis et al., 2019) **myeloid specific |
*hemoglobin associated | * fibroblast associated **pericyte marker | *endothelial related ** lymphatic endothelium associated |
*neuronal related (Zeisel et al., 2018) |