Probe:	En1_riboprobe2
Probe preparation:	Antisense labelled with digoxigenin RNA
Visualized with:	Alkaline phosphatase
Assay notes:	The authors analyzed data from the Allen Developing Mouse Brain.

Structure	Level	Pattern	Image	Note
TS19: midbrain	Present	Regionally restricted	2j	A double gradiental expression of En1 overlaps with the isthmic organizer and characterizes the neighboring areas rostral and caudal to the IMB (isthmo-mesencephalic transverse boundary), penetrating maximally about one-third into the caudal basal midbrain, and less so dorsally.
TS19: midbrain-hindbrain junction	Present		2j
TS19: metencephalon	Present	Regionally restricted	2j	There is a specular En1 gradient extending into the rostral hindbrain, possibly reaching the rh1 rhombomere.

Structure	Level	Pattern	Image	Note
TS19: midbrain	Present	Regionally restricted	2k	A double gradiental expression of En1 overlaps with the isthmic organizer and characterizes the neighboring areas rostral and caudal to the IMB (isthmo-mesencephalic transverse boundary), penetrating maximally about one-third into the caudal basal midbrain, and less so dorsally.
TS19: midbrain-hindbrain junction	Present		2k
TS19: metencephalon	Present	Regionally restricted	2k	There is a specular En1 gradient extending into the rostral hindbrain, possibly reaching the rh1 rhombomere.

Structure	Level	Pattern	Image	Note
TS19: midbrain	Present	Regionally restricted	2l	A double gradiental expression of En1 overlaps with the isthmic organizer and characterizes the neighboring areas rostral and caudal to the IMB (isthmo-mesencephalic transverse boundary), penetrating maximally about one-third into the caudal basal midbrain, and less so dorsally.
TS19: midbrain-hindbrain junction	Present		2l
TS19: metencephalon	Present	Regionally restricted	2l	There is a specular En1 gradient extending into the rostral hindbrain, possibly reaching the rh1 rhombomere.

Structure	Level	Pattern	Image	Note
TS22: midbrain	Present	Regionally restricted	4h	The labeled preisthmus showed a strong subpial signal, a moderate to weak signal at intermediate levels, and a strong signal medially.

Structure	Level	Pattern	Image	Note
TS22: midbrain	Present	Regionally restricted	4i	The labeled preisthmus showed a strong subpial signal, a moderate to weak signal at intermediate levels, and a strong signal medially.

Structure	Level	Pattern	Image	Note
TS22: midbrain	Present	Regionally restricted	4l	The labeled preisthmus showed a strong subpial signal, a moderate to weak signal at intermediate levels, and a strong signal medially.

Structure	Level	Pattern	Image	Note
TS22: midbrain	Present	Regionally restricted	4m	Signal decreased gradientally across the preisthmus, barely reaching the caudal sulcal area.

Structure	Level	Pattern	Image	Note
TS22: midbrain	Present	Regionally restricted	4n	Signal decreased gradientally across the preisthmus, barely reaching the caudal sulcal area.

Structure	Level	Pattern	Image	Note
TS22: midbrain	Present		4o

Structure	Level	Pattern	Image	Note
TS22: midbrain	Present		4p

Structure	Level	Pattern	Image	Note
TS22: midbrain	Present		4q

Structure	Cell Type	Level	Pattern	Image	Note
TS22: midbrain	dopaminergic neuron	Strong	Regionally restricted	4r	A strong medial signal related to the generation and migration of dopaminaergic neurons of the ventral tegmental area and substantia nigra.

Structure	Cell Type	Level	Pattern	Image	Note
TS22: midbrain	dopaminergic neuron	Strong	Regionally restricted	4s	A strong medial signal related to the generation and migration of dopaminaergic neurons of the ventral tegmental area and substantia nigra.

Structure	Level	Pattern	Image	Note
TS23: midbrain	Present	Regionally restricted	7y	Expression in the superficial preisthmic mantle stratum was detected in a curved shape above the isthmic superficial elements with a ventral head-like thickening (oriented topographically rostral) and a longer dorsal tail portion (oriented topographically caudal).

Structure	Level	Pattern	Image	Note
TS24: midbrain	Present	Regionally restricted	11e	At E16.5, the toral area is positive jointly with the preisthmus.

Structure	Level	Pattern	Image	Note
TS25: midbrain	Present	Regionally restricted	11f	Signal was detected in the mantle layer of the toral bulges.

Structure	Level	Pattern	Image	Note
TS26: midbrain	Present	Regionally restricted	11g	Signal was detected in the toral bulges.

Structure	Level	Pattern	Image	Note
TS26: midbrain	Present	Regionally restricted	11h	Signal was detected in the toral bulges.

Structure	Level	Pattern	Image	Note
TS27: midbrain	Present	Regionally restricted	13a	Massive labeling was detected at the toral region and decreased somewhat into the adjacent preisthmus.
TS27: inferior colliculus	Absent		13a
TS27: periaqueductal grey	Present		13a

Structure	Level	Pattern	Image	Note
TS27: midbrain	Present	Regionally restricted	13b	Massive labeling was detected at the toral region and decreased somewhat into the adjacent preisthmus.
TS27: inferior colliculus	Absent		13b
TS27: periaqueductal grey	Present		13b

Structure	Level	Pattern	Image	Note
TS27: midbrain	Present	Regionally restricted	13c	Massive labeling was detected at the toral region and decreased somewhat into the adjacent preisthmus.
TS27: inferior colliculus	Absent		13c
TS27: periaqueductal grey	Present		13c