Probe:	Sox9 cDNA3
Probe preparation:	Antisense labelled with S35 RNA
Visualized with:	Autoradiography
Assay notes:	Data not shown was indicated in the text and in the summary in Fig. 5.

Structure	Level	Pattern	Image	Note
TS11: node	Present		3A
TS11: notochordal plate	Present		3A
TS11: embryo mesoderm	Present	Regionally restricted	3A	Expression was detected in the mesoderm lateral to the node.

Structure	Level	Pattern	Image	Note
TS13: head mesenchyme derived from neural crest	Present	Regionally restricted	3C	Expression was strong in the mesenchyme subjacent to the surface ectoderm and the epidermal placodes at the mid- and hindbrain level.
TS13: head paraxial mesenchyme	Moderate		3C
TS13: notochord	Present		3C	Coexpression with Col2a1 was noted.
TS13: surface ectoderm	Strong		3C
TS13: neural crest	Present	Regionally restricted	3C	Expression was detected in the crest region of the cephalic neural plate.
TS13: otic placode	Present		3C

Structure	Level	Pattern	Image	Note
TS15: trunk sclerotome	Present	Regionally restricted	3E	Expression was detected in the sclerotome of the lower trunk somites. Coexpression with Col2a1 was noted.
TS15: trunk dermomyotome	Weak		3E

Structure	Level	Pattern	Image	Note
TS19: vertebral pre-cartilage condensation	Present	Regionally restricted	3G	Expression was detected in the mesenchymal condensation for prevertebrae.
TS19: urogenital ridge	Strong		3G

Structure	Level	Pattern	Image	Note
TS23: metatarsus mesenchyme	Present	Regionally restricted	3I	Expression was detected in the chondrogenic mass of the tarsals and metatarsals.
TS23: tarsus	Present	Regionally restricted	3I	Expression was detected in the chondrogenic mass of the tarsals and metatarsals.

Structure	Level	Pattern	Image	Note
TS22: vertebral cartilage condensation	Present	Regionally restricted	3K	Expression was detected in the chondrocytes of the lower trunk vertebrae. Coexpression with Col2a1 was noted.
TS22: intervertebral disc	Weak	Regionally restricted	3K	There was diminished expression in the intervertebral tissues. Coexpression with Col2a1 was noted.

Structure	Level	Pattern	Image	Note
TS24: basioccipital bone	Present	Regionally restricted	3M	Expression was detected in proliferating chondrocytes of the basioccipital bone. Expression was almost at background levels in hypertrophic chondrocytes.

Structure	Level	Pattern	Image	Note
TS13: future prosencephalon	Present
TS13: somite	Present
TS13: neural ectoderm	Present	Regionally restricted		Expression was detected in the neural tube.

Structure	Level	Pattern	Image	Note
TS15: branchial arch	Present
TS15: common atrial chamber endocardial lining	Present
TS15: future forebrain	Present
TS15: gut	Present
TS15: head mesenchyme	Present
TS15: limb mesenchyme	Present
TS15: somite	Present
TS15: central nervous system	Present	Regionally restricted		Expression was detected in the neural tube.

Structure	Level	Pattern	Image	Note
TS17: branchial arch	Present
TS17: forebrain ventricular layer	Present
TS17: gut	Present
TS17: head mesenchyme	Present
TS17: hindbrain ventricular layer	Present
TS17: limb mesenchyme	Present
TS17: midbrain ventricular layer	Present
TS17: notochord	Present
TS17: otocyst	Present
TS17: somite	Present
TS17: urogenital ridge	Present
TS17: respiratory system	Present			Expression was detected in bronchopulmonary tissues, larynx, and bronchial cartilage.
TS17: central nervous system	Present	Regionally restricted		Expression was detected in the neural tube.

Structure	Level	Pattern	Image	Note
TS19: inner ear epithelium	Absent			Transcripts were not detected in sensory epithelium of the inner ear.
TS19: inner ear	Present	Regionally restricted		Expression was detected in the otic vesicle.
TS19: atrioventricular canal	Present
TS19: branchial arch	Present
TS19: endocardial cushion	Present
TS19: endocardial lining	Present
TS19: gut	Present
TS19: head mesenchyme	Present
TS19: jaw primordium	Present
TS19: limb mesenchyme	Present
TS19: notochord	Present
TS19: somite	Present
TS19: respiratory system	Present			Expression was detected in bronchopulmonary tissues, larynx, and bronchial cartilage.
TS19: central nervous system	Present	Regionally restricted		Expression was detected in the neural tube.

Structure	Level	Pattern	Image	Note
TS20: atrioventricular canal	Present
TS20: cranium	Present
TS20: endocardial cushion	Present
TS20: endocardial lining	Present
TS20: gut	Present
TS20: head mesenchyme	Present
TS20: jaw primordium	Present
TS20: limb mesenchyme	Present
TS20: notochord	Present
TS20: somite	Present
TS20: urogenital ridge	Present
TS20: respiratory system	Present			Expression was detected in bronchopulmonary tissues, larynx, and bronchial cartilage.
TS20: central nervous system	Present	Regionally restricted		Expression was detected in the neural tube.

Structure	Level	Pattern	Image	Note
TS21: cranium	Present	Regionally restricted		Expression was concentrated mostly in the endocranium.
TS21: endocardial tissue	Present
TS21: facial bone primordium	Present
TS21: head mesenchyme	Present
TS21: jaw	Present
TS21: jaw skeleton	Present
TS21: limb mesenchyme	Present
TS21: somite	Present
TS21: urogenital ridge	Present
TS21: respiratory system	Present			Expression was detected in bronchopulmonary tissues, larynx, and bronchial cartilage.
TS21: central nervous system	Present	Regionally restricted		Expression was detected in the neural tube.

Structure	Level	Pattern	Image	Note
TS22: respiratory system	Present	Regionally restricted		Expression was detected in bronchopulmonary tissues and bronchial cartilage.
TS22: cranium	Present
TS22: endocardial tissue	Present
TS22: gut	Present
TS22: head mesenchyme	Present
TS22: jaw	Present
TS22: larynx	Present
TS22: limb mesenchyme	Present
TS22: somite	Present
TS22: central nervous system	Present	Regionally restricted		Expression was detected in the neural tube.

Structure	Level	Pattern	Image	Note
TS23: cranium	Present
TS23: endocardial tissue	Present
TS23: gut	Present
TS23: head mesenchyme	Present
TS23: jaw	Present
TS23: larynx	Present
TS23: limb mesenchyme	Present
TS23: limb skeleton	Present
TS23: main bronchus cartilage	Present
TS23: vertebra	Present

Structure	Level	Pattern	Image	Note
TS24: cranium	Present
TS24: forebrain ventricular layer	Present
TS24: head mesenchyme	Present
TS24: hindbrain ventricular layer	Present
TS24: jaw	Present
TS24: larynx	Present
TS24: limb mesenchyme	Present
TS24: limb skeleton	Present
TS24: main bronchus cartilage	Present
TS24: midbrain ventricular layer	Present
TS24: vertebra	Present
TS24: endocardial cushion	Weak

Structure	Level	Pattern	Image	Note
TS25: skeleton	Weak			Expression progressively diminished in most skeletal tissues.
TS25: inner ear epithelium	Absent			Transcripts were not detected in sensory epithelium of the inner ear.
TS25: cranium	Present
TS25: head mesenchyme	Present
TS25: jaw	Present
TS25: larynx	Present
TS25: main bronchus cartilage	Present
TS25: vertebra	Present

Structure	Level	Pattern	Image	Note
TS26: femur	Present	Regionally restricted		Expression was found only in small clusters of chondrocytes.
TS26: larynx	Present	Regionally restricted		Expression was found only in small clusters of chondrocytes.
TS26: vertebra	Present	Regionally restricted		Expression was found only in small clusters of chondrocytes.
TS26: mandible	Present	Regionally restricted		Expression was found in some osteoblasts.
TS26: maxilla	Present	Regionally restricted		Expression was found in some osteoblasts.
TS26: main bronchus cartilage	Present

Structure	Level	Pattern	Image	Note
TS15: neural tube roof plate	Strong		6A
TS15: neural tube lateral wall	Strong	Regionally restricted	6A	Expression was strong in the alar plate of the closed neural tube.
TS15: notochord	Present		6A
TS15: sclerotome	Present		6A

Structure	Level	Pattern	Image	Note
TS15: otocyst epithelium	Present		6C
TS15: paraxial mesenchyme	Weak		6C

Structure	Level	Pattern	Image	Note
TS19: hindbrain roof plate	Present		6E
TS19: hindbrain ventricular layer	Present		6E

Structure	Level	Pattern	Image	Note
TS19: ventricle endocardial lining	Present		6G
TS19: endocardial cushion	Present	Regionally restricted	6G	Expression was detected in the endocardial cushions flanking the atrioventricular canals.
TS19: branchial arch mesenchyme	Strong		6G

Structure	Level	Pattern	Image	Note
TS11: ectoplacental cone	Present
TS11: primitive endoderm	Absent

Structure	Level	Pattern	Image	Note
TS19: intestine	Present	Regionally restricted		Expression was detected in the intestine mucosa.
TS19: umbilical cord	Present

Structure	Level	Pattern	Image	Note
TS20: bronchus epithelium	Present
TS20: lung mesenchyme	Present
TS20: umbilical cord	Present
TS20: urogenital ridge	Present	Regionally restricted		Expression was detected in genital ridge mesenchyme.
TS20: metanephros	Present	Regionally restricted		Expression was detected in metanephric tubules.

Structure	Level	Pattern	Image	Note
TS22: pancreas	Present	Regionally restricted		Expression was detected in ductal epithelium but not in islets.
TS22: genital tubercle	Present	Regionally restricted		Expression was detected in genital tubercle mesenchyme.

Structure	Level	Pattern	Image	Note
TS23: pancreas	Present	Regionally restricted		Expression was detected in ductal epithelium.

Structure	Level	Pattern	Image	Note
TS24: intestine mucosa	Present
TS24: intestine	Present	Regionally restricted		Expression was detected in the intestine submucosa.

Structure	Level	Pattern	Image	Note
TS25: cornea	Absent