Probe:	Foxj3 cDNA1
Probe preparation:	Antisense RNA
Assay notes:	Two probes were described that gave identical results; either probe MGI:3526889 or MGI:5544118 could have been used for this assay.

Structure	Level	Pattern	Image	Note
TS13: neural ectoderm	Present	Regionally restricted	2A	Expression was detected in the neural tube.
TS13: migrating neural crest	Present	Regionally restricted	2A	Expression was detected in cells ventrolaterally of the neural tube, likely to be migrating cranial neural crest.

Structure	Level	Pattern	Image	Note
TS15: forelimb bud	Present		2B
TS15: future brain	Present		2B
TS15: optic vesicle	Present		2B
TS15: otocyst	Present		2B

Structure	Level	Pattern	Image	Note
TS17: telencephalon	Present	Regionally restricted	2C	Expression was detected in telencephalic vesicles.
TS17: 1st branchial arch mandibular component	Present		2C
TS17: 1st branchial arch maxillary component	Present		2C
TS17: 2nd branchial arch	Present		2C
TS17: forelimb bud	Present		2C
TS17: hindlimb bud	Present		2C
TS17: mesenchyme derived from neural crest	Present		2C
TS17: myotome	Present		2C
TS17: primitive ventricle	Present		2C
TS17: body wall	Present	Regionally restricted	2C	Expression was detected in a segmented pattern of diffuse patches.

Structure	Level	Pattern	Image	Note
TS17: migrating neural crest	Present	Regionally restricted	2D	Expression in migrating neural crest cells runs along the neural tube and gradually shifts from a dorsal location at the posterior to the position of the dorsal root ganglia ventrally.
TS17: telencephalon	Present		2D

Structure	Level	Pattern	Image	Note
TS19: migrating neural crest	Present	Regionally restricted	2G	Expression in migrating neural crest cells runs along the neural tube and gradually shifts from a dorsal location at the posterior to the position of the dorsal root ganglia ventrally.
TS19: heart	Absent		2G
TS19: myotome	Present		2G	There was a more distinct segmentation of the myotomes at E11.5 compared to E10.5.

Structure	Level	Pattern	Image	Note
TS17: myotome	Present		2J

Structure	Level	Pattern	Image	Note
TS20: eye	Present		2L
TS20: forelimb digit	Present		2L

Structure	Level	Pattern	Image	Note
TS20: migrating neural crest	Present	Regionally restricted	2M	There was a ventral shift in the expressing neural crest segments toward the position of the dorsal root ganglia along the craniocaudal axis.
TS20: body wall	Present	Regionally restricted	2M	Expression was detected perpendicular to the body axis in stripes along the developing body wall musculature.

Structure	Level	Pattern	Image	Note
TS17: dermomyotome	Present		3A
TS17: dorsal root ganglion	Present		3A
TS17: neural tube	Present		3A
TS17: body wall	Present	Regionally restricted	3A	Expression was detected ventrolaterally of the dorsal root ganglia.

Structure	Level	Pattern	Image	Note
TS19: dorsal root ganglion	Present		3B
TS19: myotome	Present		3B
TS19: neural tube	Present		3B
TS19: body wall	Present	Regionally restricted	3B	Expression was detected in the mesenchyme of the body wall. Staining was separated from the surface ectoderm by a layer of negative mesenchyme.
TS19: embryo mesenchyme	Present	Regionally restricted	3B	Expression was detected in the mesenchyme of the body wall. Staining was separated from the surface ectoderm by a layer of negative mesenchyme.

Structure	Level	Pattern	Image	Note
TS19: dorsal root ganglion	Present		3E
TS19: myotome	Present		3E

Structure	Level	Pattern	Image	Note
TS19: dorsal root ganglion	Present		3H
TS19: myotome	Present		3H

Structure	Level	Pattern	Image	Note
TS19: mandibular process	Present		3K
TS19: maxillary process	Present		3K

Structure	Level	Pattern	Image	Note
TS20: lens vesicle	Present	Regionally restricted	3M	Expression was restricted to the anterior hemisphere of the lens.
TS20: retina	Present	Regionally restricted	3M	Expression was restricted to the medial part of the retina.

Structure	Level	Pattern	Image	Note
TS19: acoustic ganglion	Present		3N
TS19: facial ganglion	Present		3N
TS19: hindbrain	Present		3N
TS19: trigeminal ganglion	Present		3N
TS19: inner ear	Present	Regionally restricted	3N	Expression was detected in the otocyst.

Structure	Level	Pattern	Image	Note
TS20: dorsal root ganglion	Present		3P
TS20: spinal cord	Present		3P
TS20: body wall	Present	Regionally restricted	3P	Expression was detected in the body wall musculature. Staining was separated from the surface ectoderm by a layer of negative mesenchyme.
TS20: skeletal muscle	Present	Regionally restricted	3P	Expression was detected in the body wall musculature. Staining was separated from the surface ectoderm by a layer of negative mesenchyme.

Structure	Level	Pattern	Image	Note
TS17: limb mesenchyme	Present	Regionally restricted	4A	Expression was detected in a subectodermal mesenchymal layer and in an internal zone.
TS17: apical ectodermal ridge	Absent		4A
TS17: limb ectoderm	Absent		4A	No expression was detected in the surface ectoderm.

Structure	Level	Pattern	Image	Note
TS19: limb mesenchyme	Present	Regionally restricted	4B	The two zones of expression can no longer be distinguished. The staining is concentrated to interior mesenchyme that, in the distal part, follows the outline of the forming digital rays.

Structure	Level	Pattern	Image	Note
TS20: forearm mesenchyme	Present		4C
TS20: forelimb digit mesenchyme	Present		4C
TS20: hand mesenchyme	Present		4C

Structure	Level	Pattern	Image	Note
TS17: limb mesenchyme	Present	Regionally restricted	4D	Expression was detected in a subectodermal mesenchymal layer and in an internal zone.

Structure	Level	Pattern	Image	Note
TS19: limb mesenchyme	Present	Regionally restricted	4E	The two zones of expression can no longer be distinguished. The staining is concentrated to interior mesenchyme.

Structure	Level	Pattern	Image	Note
TS20: forelimb digit mesenchyme	Present		4F