Probe:	probe 1
Probe preparation:	labelled with S35 RNA
Visualized with:	Autoradiography
Assay notes:	Hybridization using the Hox-2.9 sense strand was routinely included as a negative control; specific hybridization was not observed.

Structure	Level	Pattern	Image	Note
TS11: primitive streak	Present		5A	Expression along length of primitive streak.
TS11: embryo mesoderm	Present	Regionally restricted	5A	Expression in mesoderm in posterior half of embryo.
TS11: embryo	Present	Regionally restricted	5A	No expression in anterior half of embryo.

Structure	Level	Pattern	Image	Note
TS11: embryo ectoderm	Absent		5B/C	No expression in embryonic ectoderm outside of primitive streak.

Structure	Level	Pattern	Image	Note
TS12: primitive streak	Strong		6A/B	Abundant expression along length of primitive streak.
TS12: embryo mesenchyme	Weak	Regionally restricted	6A/B	Expression is found in mesoderm anterior of archenteron. Transcripts are not detected in region anterior of primitive hindbrain.
TS12: embryo ectoderm	Present	Regionally restricted	6A/B	Transcripts are detected in ectodermal cells anterior of primitive streak, although only in cells at or posterior to leading edge of expression in mesoderm.
TS12: neural ectoderm	Present	Graded	6A/B	Anterior of archenteron, expression is highest at rostral end of region, in a stripe about 8-12 cell diameters in length along A-P axis in a caudal part of head fold. Transcripts are not detected anterior of neuromere B.

Structure	Level	Pattern	Image	Note
TS12: embryo ectoderm	Present	Regionally restricted	6C/D	Expression in ectodermal cells lateral to primitive streak, only in cells at or posterior to leading edge of expression in mesoderm.

Structure	Level	Pattern	Image	Note
TS13: future spinal cord neural plate	Present	Regionally restricted	7A/B	In posterior part of embryo, transcripts are found along length of neural plate and primitive streak/tail bud, but are not detected in more ventral structures.
TS13: primitive streak	Present	Regionally restricted	7A/B	In posterior part of embryo, transcripts are found along length of neural plate and primitive streak/tail bud, but are not detected in more ventral structures.
TS13: embryo	Strong	Regionally restricted	7A/B	Highest levels of expression in tail bud.
TS13: embryo mesenchyme	Weak	Regionally restricted	7A/B	Anterior of primitive streak, lower levels of expression in mesoderm and neural tube.
TS13: neural tube	Weak	Regionally restricted	7A/B	Anterior of primitive streak, lower levels of expression in mesoderm and neural tube.
TS13: embryo ectoderm	Present	Regionally restricted	7A/B	In dorsal aspect of 2nd branchial arch unit, expression in 'thin' ectoderm just lateral to neural tube.
TS13: branchial arch mesenchyme	Present	Regionally restricted	7A/B	In ventral aspect of 3rd branchial arch unit, expression in lateral mesoderm.
TS13: branchial arch ectoderm	Present	Regionally restricted	7A/B	Expression in surface ectoderm in caudal half of 2nd branchial cleft.
TS13: 2nd branchial pouch endoderm	Present	Regionally restricted	7A/B	Expression in endoderm in caudal half of 2nd pharyngeal pouch.
TS13: foregut diverticulum	Present	Regionally restricted	7A/B	In ventral aspect of 3rd branchial arch unit, expression in wall of foregut posterior to pouch

Structure	Level	Pattern	Image	Note
TS13: embryo mesenchyme	Weak	Regionally restricted	7C/D	Anterior of primitive streak, lower levels of expression in mesoderm and neural tube.
TS13: neural tube	Weak	Regionally restricted	7C/D	Anterior of primitive streak, lower levels of expression in mesoderm and neural tube.
TS13: embryo endoderm	Absent		7C/D	No expression in posterior lateral plate mesoderm and endoderm.
TS13: lateral plate mesoderm	Absent		7C/D	No expression in posterior lateral plate mesoderm and endoderm.

Structure	Level	Pattern	Image	Note
TS13: embryo mesenchyme	Weak	Regionally restricted	7E/F	Anterior of primitive streak, lower levels of expression in mesoderm.
TS13: intermediate mesenchyme	Absent		7E/F	As rostral end of presomitic mesoderm condenses into somites, expression abruptly ceases in paraxial and intermediate mesoderm.
TS13: trunk paraxial mesenchyme	Absent		7E/F	As rostral end of presomitic mesoderm condenses into somites, expression abruptly ceases in paraxial and intermediate mesoderm.
TS13: lateral plate mesoderm	Present		7E/F	Expression still detectable in lateral plate mesoderm.
TS13: neural tube	Strong		7E/F	Relatively high levels of expression in neural tube.
TS13: trunk somite	Absent		7E/F	No expression in the most recently condensed somite

Structure	Level	Pattern	Image	Note
TS13: rhombomere 4	Present		8A	In dorsal aspect of 2nd branchial arch, expression in hindbrain neuroectoderm restricted to region, anterior of otic invagination, giving rise to rhombomere 4.
TS13: head mesenchyme	Present		8A
TS13: future spinal cord neural crest	Present		8A

Structure	Level	Pattern	Image	Note
TS13: embryo ectoderm	Present	Regionally restricted	8B/C	In dorsal aspect of 2nd branchial arch, expression in 'thin' ectoderm just lateral to neural tube.
TS13: 2nd branchial arch mesenchyme derived from neural crest	Present	Regionally restricted	8B/C	Expression in dorsal neural crest of 2nd branchial arch.
TS13: lateral plate mesoderm	Present		8B/C
TS13: 2nd branchial arch mesenchyme	Weak	Regionally restricted	8B/C	Greatly decreased expression levels in 2nd arch cranial (paraxial) mesoderm.
TS13: branchial arch mesenchyme	Present	Regionally restricted	8B/C	In ventral aspect of 3rd branchial arch, expression in lateral mesoderm.
TS13: branchial arch ectoderm	Present	Regionally restricted	8B/C	Expression in urface ectoderm in caudal half of 2nd branchial cleft.
TS13: 2nd branchial pouch	Present	Regionally restricted	8B/C	Expression in endoderm in caudal half of 2nd pharyngeal pouch.
TS13: foregut diverticulum	Present	Regionally restricted	8B/C	In ventral aspect of the 3rd branchial arch, expression in wall of foregut posterior to pouch

Structure	Level	Pattern	Image	Note
TS13: embryo ectoderm	Present	Regionally restricted	8D/E	In dorsal aspect of 2nd branchial arch, expression in 'thin' ectoderm just lateral to neural tube.
TS13: neural crest	Present		8D/E
TS13: future spinal cord neural crest	Present	Regionally restricted	8D/E	High level of expression in dorsal neural crest of 2nd branchial arch. No expression in older neural crest cells, which has mostly migrated ventrally to 2nd branchial arch.

Structure	Level	Pattern	Image	Note
TS15: rhombomere 4	Strong		9A/B
TS15: head mesenchyme	Absent		9A/B
TS15: pharynx	Strong	Regionally restricted	9A/B	Abundant expression in endoderm of pharynx.
TS15: embryo mesenchyme	Strong	Regionally restricted	9A/B	Abundant expression in lateral plate mesoderm.

Structure	Level	Pattern	Image	Note
TS15: rhombomere 4	Strong		9C/D
TS15: neural tube floor plate	Absent		9C/D

Structure	Level	Pattern	Image	Note
TS15: 2nd branchial arch mesenchyme derived from neural crest	Present	Regionally restricted	9E/F	Expression in dorsal aspect of 2nd branchial arch.
TS15: 3rd branchial arch	Present	Regionally restricted	9E/F	No expression in ventral aspect of 3rd branchial arch.
TS15: branchial arch	Present	Regionally restricted	9E/F	Expression in 4th branchial arch.
TS15: 3rd branchial groove ectoderm	Strong	Regionally restricted	9E/F	Abundant expression in caudal half of 3rd branchial cleft (surface ectoderm).
TS15: 3rd branchial pouch	Strong	Regionally restricted	9E/F	Abundant expression in caudal half of 3rd pharyngeal pouch,
TS15: pharynx	Strong	Regionally restricted	9E/F	Abundant expression in surrounding walls of pharynx, posterior to developing thyroid, but anterior to lung bud.
TS15: embryo mesenchyme	Weak	Regionally restricted	9E/F	Lower levels of expresion in lateral plate mesoderm (gut-associated) near the 3rd pouch.
TS15: embryo endoderm	Weak	Regionally restricted	9E/F	Low levels of expression in more posterior tissues of endodermal origin.

Structure	Level	Pattern	Image	Note
TS15: tail	Present

Structure	Level	Pattern	Image	Note
TS17: rhombomere 4	Present	Regionally restricted		Expression largely restricted to 4th rhombomere, in both germinal and intermediate layers.
TS17: embryo	Weak	Regionally restricted		Very low levels of expression in endoderm and mesoderm structures that were positive for expression at E9.5.
TS17: mesenchyme derived from neural crest	Absent