Probe:	Sox9 cDNA3
Probe preparation:	Antisense labelled with digoxigenin RNA

Structure	Level	Pattern	Image	Note
TS17: 1st branchial arch mesenchyme derived from neural crest	Present	Regionally restricted	1A	Expression was detected in malleus-incus condensation located in the pharyngeal arch 1 mesenchyme, lateral to the pharyngeal endoderm.
TS17: middle ear mesenchyme	Present	Regionally restricted	1A	Expression was detected in malleus-incus condensation located in the pharyngeal arch 1 mesenchyme, lateral to the pharyngeal endoderm.

Structure	Level	Pattern	Image	Note
TS18: 1st branchial arch mesenchyme derived from neural crest	Present	Regionally restricted	1D	Expression was detected in malleus-incus condensation located in the pharyngeal arch 1 mesenchyme, lateral to the pharyngeal endoderm.
TS18: middle ear mesenchyme	Present	Regionally restricted	1D	Expression was detected in malleus-incus condensation located in the pharyngeal arch 1 mesenchyme, lateral to the pharyngeal endoderm.

Structure	Level	Pattern	Image	Note
TS19: 1st branchial arch	Present	Regionally restricted	1G	Expression was detected in malleus-incus condensation located in the pharyngeal arch 1 mesenchyme, lateral to the pharyngeal endoderm.
TS19: middle ear mesenchyme	Present	Regionally restricted	1G	Expression was detected in malleus-incus condensation located in the pharyngeal arch 1 mesenchyme, lateral to the pharyngeal endoderm.

Structure	Level	Pattern	Image	Note
TS17: 2nd branchial arch mesenchyme derived from neural crest	Present	Regionally restricted	1K	In pharyngeal arch 2, stapes condensation was demarcated by Sox9 expression in mesenchyme dorsal to the pharyngeal endoderm.
TS17: middle ear mesenchyme	Present	Regionally restricted	1K	In pharyngeal arch 2, stapes condensation was demarcated by Sox9 expression in mesenchyme dorsal to the pharyngeal endoderm.

Structure	Level	Pattern	Image	Note
TS18: 2nd branchial arch mesenchyme derived from neural crest	Present	Regionally restricted	1N	In pharyngeal arch 2, stapes condensation was demarcated by Sox9 expression in mesenchyme dorsal to the pharyngeal endoderm.
TS18: middle ear mesenchyme	Present	Regionally restricted	1N	In pharyngeal arch 2, stapes condensation was demarcated by Sox9 expression in mesenchyme dorsal to the pharyngeal endoderm.

Structure	Level	Pattern	Image	Note
TS19: 2nd branchial arch mesenchyme derived from neural crest	Present	Regionally restricted	1Q	In pharyngeal arch 2, stapes condensation was demarcated by Sox9 expression in mesenchyme dorsal to the pharyngeal endoderm. At E11.5, expression was downregulated in the center of the stapes condensation region.
TS19: middle ear mesenchyme	Present	Regionally restricted	1Q	In pharyngeal arch 2, stapes condensation was demarcated by Sox9 expression in mesenchyme dorsal to the pharyngeal endoderm. At E11.5, expression was downregulated in the center of the stapes condensation region.

Structure	Level	Pattern	Image	Note
TS20: ossicle pre-cartilage condensation	Present	Regionally restricted	1U	Sox9 expression is a single domain in the malleus-incus region and a separate domain in the stapes region.

Structure	Level	Pattern	Image	Note
TS21: incus pre-cartilage condensation	Present		1X	At E13.5, the malleus and incus split into two separate Sox9 expression domains.
TS21: malleus pre-cartilage condensation	Present		1X	At E13.5, the malleus and incus split into two separate Sox9 expression domains.
TS21: stapes pre-cartilage condensation	Present		1X

Structure	Level	Pattern	Image	Note
TS17: 1st branchial arch mesenchyme derived from neural crest	Present	Regionally restricted	2A	Expression was detected in malleus-incus region in pharyngeal arch 1.
TS17: middle ear mesenchyme	Present	Regionally restricted	2A	Expression was detected in malleus-incus region in pharyngeal arch 1.

Structure	Level	Pattern	Image	Note
TS19: 1st branchial arch	Present	Regionally restricted	2C	Expression was detected in malleus-incus condensation located in the pharyngeal arch 1 mesenchyme.
TS19: middle ear mesenchyme	Present	Regionally restricted	2C	Expression was detected in malleus-incus condensation located in the pharyngeal arch 1 mesenchyme.

Structure	Level	Pattern	Image	Note
TS17: 1st branchial arch mesenchyme derived from neural crest	Present	Regionally restricted	2F	The expression pattern in the mutant malleus-incus region in pharyngeal arch 1 was similar to control.
TS17: middle ear mesenchyme	Present	Regionally restricted	2F	The expression pattern in the mutant malleus-incus region in pharyngeal arch 1 was similar to control.

Structure	Level	Pattern	Image	Note
TS19: 1st branchial arch	Present	Regionally restricted	2H	The expression pattern in the mutant malleus-incus region in pharyngeal arch 1 was similar to control.
TS19: middle ear mesenchyme	Present	Regionally restricted	2H	The expression pattern in the mutant malleus-incus region in pharyngeal arch 1 was similar to control.

Structure	Level	Pattern	Image	Note
TS17: 2nd branchial arch mesenchyme derived from neural crest	Present	Regionally restricted	2L	In pharyngeal arch 2, stapes condensation was demarcated by Sox9 expression in mesenchyme dorsal to the pharyngeal endoderm.
TS17: middle ear mesenchyme	Present	Regionally restricted	2L	In pharyngeal arch 2, stapes condensation was demarcated by Sox9 expression in mesenchyme dorsal to the pharyngeal endoderm.

Structure	Level	Pattern	Image	Note
TS19: 2nd branchial arch mesenchyme derived from neural crest	Present	Regionally restricted	2N	In pharyngeal arch 2, stapes condensation was demarcated by Sox9 expression in mesenchyme dorsal to the pharyngeal endoderm. At E11.5, expression was downregulated in the center of the stapes condensation region.
TS19: middle ear mesenchyme	Present	Regionally restricted	2N	In pharyngeal arch 2, stapes condensation was demarcated by Sox9 expression in mesenchyme dorsal to the pharyngeal endoderm. At E11.5, expression was downregulated in the center of the stapes condensation region.

Structure	Level	Pattern	Image	Note
TS17: 2nd branchial arch mesenchyme derived from neural crest	Weak	Regionally restricted	2Q	Mutant expression in pharyngeal arch 2, stapes condensation was weaker at E10.5
TS17: middle ear mesenchyme	Weak	Regionally restricted	2Q	Mutant expression in pharyngeal arch 2, stapes condensation was weaker at E10.5

Structure	Level	Pattern	Image	Note
TS19: 2nd branchial arch mesenchyme derived from neural crest	Present	Regionally restricted	2S	Mutant expression in pharyngeal arch 2, stapes condensation at E11.5 was similar to control embryos.
TS19: middle ear mesenchyme	Present	Regionally restricted	2S	Mutant expression in pharyngeal arch 2, stapes condensation at E11.5 was similar to control embryos.

Structure	Level	Pattern	Image	Note
TS20: ossicle pre-cartilage condensation	Present	Regionally restricted	2W	Expression was detected in the malleus-incus region and in the stapes region. A hole was observed in the center of the stapes region.

Structure	Level	Pattern	Image	Note
TS20: ossicle pre-cartilage condensation	Present	Regionally restricted	2Aa	Expression was detected in the malleus-incus region and in the stapes region. No hole was observed in the center of the stapes region of the mutant.

Structure	Level	Pattern	Image	Note
TS22: incus cartilage condensation	Present		3A
TS22: malleus cartilage condensation	Present		3A
TS22: stapes cartilage condensation	Present		3A	Control displays the stapedial foramen hole in the stapes.

Structure	Level	Pattern	Image	Note
TS22: incus cartilage condensation	Present		3D
TS22: malleus cartilage condensation	Present		3D
TS22: stapes cartilage condensation	Present		3D	The stapedial foramen hole was not seen in the mutant staining.

Structure	Level	Pattern	Image	Note
TS17: middle ear mesenchyme	Present	Regionally restricted	4B	Expression was detected in the prospective stapes region.

Structure	Level	Pattern	Image	Note
TS17: middle ear mesenchyme	Weak	Regionally restricted	4F	Expression was largely diminished in the prospective stapes region of the conditional mutant.