Antibody:	Anti-Spatial-alpha
Detection system:	Secondary antibody coupled to Alexa Fluor

Structure	Level	Pattern	Image	Note
TS20: thymus primordium	Present	Regionally restricted	1B Merge E12.5 , 1B Spatial E12.5	Expression was detected in the whole epithelium where it overlapped with Krt5 and Krt8.

Structure	Cell Type	Level	Pattern	Image	Note
TS23: thymus primordium	epithelial cell of thymus	Present	Regionally restricted	1B Merge E15.5 , 1B Spatial E15.5	Smaller clusters of thymic epithelial cells were identified as Krt8+Krt5-, as well as Krt8-Krt5+. Expression of Tbata was detected in both sets of clusters. Additionally, some Tbata+ cells were Krt8+Krt5+.

Structure	Level	Pattern	Image	Note
TS20: thymus primordium	Present	Regionally restricted	1C Spatial E12.5 , 1C Merge E12.5	Expression colocalized with the epithelial progenitor cell marker MTS24 and was found in some MTS24-negative population.

Structure	Cell Type	Level	Pattern	Image	Note
TS23: thymus primordium	epithelial cell of thymus	Present	Regionally restricted	1C Merge E15.5 , 1C Spatial E15.5	Expression colocalized with the epithelial progenitor cell marker MTS24.
TS23: thymus primordium		Present	Regionally restricted	1C Spatial E15.5 , 1C Merge E15.5	Expression was found in some MTS24-negative population.

Structure	Cell Type	Level	Pattern	Image	Note
TS28: thymus medulla epithelium	medullary thymic epithelial cell	Present		1C Merge Adult , 1C Spatial Adult	Expression colocalized with MTS24+ population of medullary thymic epithelial cells.

Structure	Cell Type	Level	Pattern	Image	Note
TS28: thymus subcapsular epithelium	epithelial cell of thymus	Present		1D C57BL/6J bottom	Expressing thymic epithelial cells are mainly concentrated in the subcapsular region of the adult thymus.
TS28: thymus cortex epithelium	cortical thymic epithelial cell	Present		1D C57BL/6J bottom	Expression in the cortex is diluted due to the presence of thymocytes.

Structure	Cell Type	Level	Pattern	Image	Note
TS28: thymus epithelium	epithelial cell of thymus	Present		1D CD3e-/- bottom	Expression showed a differential distribution in the mutant.

Structure	Cell Type	Level	Pattern	Image	Note
TS28: thymus cortex epithelium	cortical thymic epithelial cell	Present		2A Merge top , 2A Spatial top , 2A inset	Expression colocalized with Krt8, a cortical thymic epithelial cell marker. It was seen in both nuclear and cytosolic compartments in the cortex.

Structure	Cell Type	Level	Pattern	Image	Note
TS28: thymus medulla epithelium	medullary thymic epithelial cell	Present		2A Spatial bottom , 2A Merge middle , 2A Spatial middle , 2A Merge bottom	Expression colocalized with MTS10, a medullary thymic epithelial cell marker. It was localized in the nucleus in the medulla.

Structure	Cell Type	Level	Pattern	Image	Note
TS28: thymus medulla epithelium	medullary thymic epithelial cell	Present		2C Spatial left , 2C Merge left	Expression colocalized with UEA1, a medullary thymic epithelial cell marker.

Structure	Cell Type	Level	Pattern	Image	Note
TS28: thymus medulla epithelium	medullary thymic epithelial cell	Present	Regionally restricted	2C Merge right , 2C Spatial right	Expression was observed in a vesicle- like localization in the nucleus that colocalized with the Aire protein, which localizes in mature medullary thymic epithelial cells.

Structure	Cell Type	Level	Pattern	Image	Note
TS28: thymus medulla epithelium	medullary thymic epithelial cell	Present	Regionally restricted	3A Merge bottom , 3A Spatial	Expression overlapped with MTS10, a medullary thymic epithelial cell marker. Expression was found in ~16% of mature medullary thymic epithelial cells that were also Aire+.

Structure	Cell Type	Level	Pattern	Image	Note
TS28: thymus medulla epithelium	medullary thymic epithelial cell	Present	Regionally restricted	3C Spatial left , 3C Merge left	Expression overlapped with MTS10, a medullary thymic epithelial cell marker.

Structure	Cell Type	Level	Pattern	Image	Note
TS28: thymus medulla epithelium	medullary thymic epithelial cell	Weak	Regionally restricted	3C Merge center , 3C Spatial center	A 28-fold reduction of staining was observed in the mutant.

Structure	Cell Type	Level	Pattern	Image	Note
TS28: thymus medulla epithelium	medullary thymic epithelial cell	Weak	Regionally restricted	3C Merge right , 3C Spatial right	A 15-fold reduction of staining was observed in the mutant.