Oocytes of a single individual of Ciona intestinalis (Roscoff, France) were fertilized by a mixture of sperm of two individuals and development was followed microscopically. Embryos were snapfrozen in liquid nitrogen at the appropriate stage and kept at -80°C. Samples at stage 0, 8, 12, 15, 21, 26 were collected from the same fertilzation, while sample from stage 11 was independently collected from a different individual. Total RNA was prepared with the RNA II kit of Magerey Nagel and the quality was checked with the Bioanalyzer, all samples had a RIN value of higher than 9. Strand specific libraries were constructed and the sequencing (50PE) was performed with Illumina HiSeq 2000 technology (BGI, Hong Kong, China). Reads were aligned onto C.robusta genome and considered to reflect the expression of the C.robusta orthologous genes.

Assay platform	Illumina HiSeq 2000
Layout	Paired-end
Stranded	Yes
Read length	49
Normalized data types	FPKM RLE
Wild type - Replica 1
	Territories	whole embryo -
	Biomaterial(s)	C. robusta formely Ciona int. type A, Stage 0 (Unfertilized egg)
		C. robusta formely Ciona int. type A, Stage 8 (64-cell)
		C. robusta formely Ciona int. type A, Stage 11 (early gastrula)
		C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)
		C. robusta formely Ciona int. type A, Stage 15 (mid neurula)
		C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)
		C. robusta formely Ciona int. type A, Stage 26 (hatching larva)
Wild type - Replica 2
	Territories	whole embryo -
	Biomaterial(s)	C. robusta formely Ciona int. type A, Stage 0 (Unfertilized egg)
		C. robusta formely Ciona int. type A, Stage 8 (64-cell)
		C. robusta formely Ciona int. type A, Stage 11 (early gastrula)
		C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)
		C. robusta formely Ciona int. type A, Stage 15 (mid neurula)
		C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)
		C. robusta formely Ciona int. type A, Stage 26 (hatching larva)

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :RAR.
Expression pattern : Unlocalized signal was detected.
Comment : Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	whole embryo -

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :RAR.
Expression pattern : No distinct zygotic signal was detected.
Comment : Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	whole embryo -

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :RAR.
Expression pattern : No distinct zygotic signal was detected.
Comment : Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	whole embryo -

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :RAR.
Expression pattern : a7.9, a7.10, a7.11, a7.12, a7.13, a7.14, a7.15, a7.16, b7.9, b7.10, b7.11, b7.12, b7.13, b7.14, b7.15, b7.16.
Comment : Maternal signal were observed ubiquitously mainly in the early cleaving stages, but also somewhat in the later stage.

Aniseed annotation;
According to the picture, the signal in b7.9 and b7.10 cell pairs is very weak.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	a line - b7.10 cell pair - b7.11 cell pair - b7.12 cell pair - b7.13 cell pair - b7.14 cell pair - b7.15 cell pair - b7.16 cell pair - b7.9 cell pair -

Animal view of a 64-cell embryo probed for Ci-RAR expression.

Original annotation:
Ci-RAR mRNA was not detected up to the 32 cell-stage. It was first detected in the nuclei of the epidermal-lineage blastomeres in the animal hemisphere.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	a line - b line -

Expression of the Nru-Z transgene in the animal hemisphere of the 64-cell embryo, as detected by in situ hybridization using a lacZ specific probe.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	a7.10 cell pair - a7.11 cell pair - a7.12 cell pair - a7.13 cell pair - a7.14 cell pair - a7.15 cell pair - a7.16 cell pair - a7.9 cell pair - b7.10 cell pair - b7.12 cell pair - b7.13 cell pair - b7.14 cell pair - b7.15 cell pair - b7.16 cell pair - b7.9 cell pair -

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :RAR.
Expression pattern : a8.17, a8.18, a8.19, a8.20, a8.21, a8.22, a8.23, a8.24, a8.25, a8.26, a8.27, a8.28, a8.29, a8.30, a8.31, a8.32, b8.18, b8.20, b8.21, b8.22, b8.23, b8.24, b8.25, b8.26, b8.27, b8.28, b8.29, b8.30, b8.31, b8.32.
Comment : Maternal signal were observed ubiquitously mainly in the early cleaving stages, but also somewhat in the later stage.

Aniseed annotation:
The signal is stronger in the a line than in the b line.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	a line - b8.18 cell pair - b8.20 cell pair - b8.21 cell pair - b8.22 cell pair - b8.23 cell pair - b8.24 cell pair - b8.25 cell pair - b8.26 cell pair - b8.27 cell pair - b8.28 cell pair - b8.29 cell pair - b8.30 cell pair - b8.31 cell pair - b8.32 cell pair -

Vegetal view of a gastrula stage embryo probed for Ci RAR expression.

Original annotation:
During gastrulation, the mRNA is observed in the anterior epidermal (ep) and endodermal (en) lineages.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	head endoderm - head epidermis -

Aniseed Comment : update of annotation of (Imai et al.,2004), based on (Imai et al.,2006).

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	anterior ventral head epidermis (a7.11 line) - dorsal midline anterior tail epidermis - dorso lateral head epidermis - lateral anterior tail epidermis - lateral posterior tail epidermis - ventral anterior tail epidermis - ventral head epidermis -

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :RAR.
Expression pattern : epidermis.
Comment : Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	whole embryo -

Ci-RAR mRNA expression in a dorsal view of a normally developing gastrula. The localization of Ci-RAR positive cells resembles that of CiHox-1 expressing cells. ep, epidermis; en, endoderm.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	anterior head endoderm - head epidermis -

Vegetal view of a gastrula stage embryo DMSO-treated probed for Ci-RAR expression.

Original annotation:
The expression pattern was almost identical to that observed in non-treated normal embryos (anterior epidermal and endodermal lineage) (en, endoderm; ep, epidermis).

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	endoderm - head epidermis -

Views of late gastrula stage showing reporter expression of the region upstream of Ci-RAR from -697bp to -394bp in mesenchyme.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)

Dorsal view of an early neurula stage embryo probed for the expression of Ci-RAR mRNA. Ci-Hox and Ci-RAR expression patterns were similar. en, endoderm.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central head endoderm (B7.1 line) - head epidermis -

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :RAR.
Expression pattern : nervous system, endoderm.
Comment : Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	endoderm - neural plate -

Lateral view of an early neurula stage embryo DMSO treated and probed for Ci-RAR.

Original annotation:
In DMSO-treated control embryos, the expression pattern of Ci-RAR mRNA was almost identical to that observed in non-treated embryos during gastrulation and neurulation (head endoderm epidermis, nerve cord) (en, endoderm, nc, nerve cord, ep, epidermis).

Aniseed annotation:
Progenitors of the nerve cord are row I neural plate and b10.73, b10.74 cell pairs at neurula stage.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	b10.73 cell pair - b10.74 cell pair - epidermis - head endoderm - row I neural plate -

Lateral view of a neurula stage embryo probed for Ci-RAR expression.

Original annotation:
Ci-RAR expression persists in the head endoderm (en). The expression in the epidermis gradually became undetectable. Nerve cord (nc) is also stained.

Aniseed annotation:
Progenitors of the nerve cord are row I neural plate and b10.73, b10.74 cell pairs at neurula stage.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	b10.73 cell pair - b10.74 cell pair - epidermis - head endoderm - row I neural plate -

Lateral view of a tailbud embryo electroporated with Ci-RAR cis-regulatory region in which region from -953 to -218 and region from -972 to -963 were deleted, upstream a LacZ reporter gene (construct named MA2-Z in the paper). The most anterior region of the DME derived from the a8.26 blastomere pairs is indicated by a blue bracket.

Original annotation:
The lacZ mRNA was also detected in the dorsal midline epidermis (DME) when MA2-Z was introduced (NC, nerve cord).

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - tail nerve cord -

Lateral view of a tailbud embryo electroporated with Ci-RAR cis-regulatory region in which region from -953 to -218 and region from -1002 to -986 were deleted, upstream a LacZ reporter gene (construct named MA3-Z in the paper). The most anterior region of the DME derived from the a8.26 blastomere pairs is indicated by a blue bracket.

Original annotation:
Electroporation of MA3-Z did not result in the expression of lacZ in the dorsal midline epidermis (DME). In this case, the expression of lacZ was observed in some other tissues, indicating that the embryos surely carried the transgene (BR, brain; NC, nerve cord; VE, ventral epidermis).

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	neck - posterior sensory vesicle - tail muscles - tail nerve cord - ventral head epidermis - visceral ganglion -

Lateral view of a tailbud embryo electroporated with Ci-RAR cis-regulatory region in which region from -953 to -218 and region from -986 to -982 were deleted, upstream a LacZ reporter gene (construct named MA4-Z in the paper). The most anterior region of the DME derived from the a8.26 blastomere pairs is indicated by a blue bracket.

Original annotation:
The lacZ mRNA was detected in the dorsal midline epidermis (DME) when MA4-Z was introduced.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - tail muscles - tail nerve cord - ventral midline posterior tail epidermis -

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :RAR.
Expression pattern : nervous system, nerve cord, endoderm.
Comment : Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.

Aniseed annotation :
A staining has been detected in part of the central nervous system, and also in the tail muscles.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central nervous system - head endoderm - tail muscles -

Lateral and dorsal views of an early tailbud stage embryo probed for Ci RAR expression.

Original annotation: :
Two discrete regions of the nerve cord (nc), neck region and the middle part of tail muscle cells (mu) were stained. Head endoderm (en) is also stained. The expression in the epidermis gradually became undetectable.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	head endoderm - neck - tail muscles - tail nerve cord - ventral head epidermis -

Lateral view of an early tailbud stage embryo DMSO-treated probed for Ci-RAR expression. The dorsal side is up.

Original annotation:
In DMSO-treated control embryos, the expression pattern of Ci-RAR mRNA was almost identical to that observed in non-treated normal embryos (head endoderm, muscle, part of tail nerve cord, neck) (nc, nerve cord; en, endoderm; mu, muscle).

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	head endoderm - neck - tail muscles - tail nerve cord - ventral head epidermis -

Deletion analyses revealed that 1,326 bp of the 5 prime flanking region of Ci-RAR was sufficient for driving the lacZ expression in the CNS, epidermis, and muscle, where endogenous Ci-RAR gene expression was observed. (No picture was provided)

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central nervous system - epidermis - tail muscles -

Deletion analyses revealed that 1,326 bp of the 5 prime flanking region of Ci-RAR was sufficient for driving the lacZ expression in the CNS, epidermis, and muscle, where endogenous Ci-RAR gene expression was observed. br, brain; ep, epidermis; mu, muscle; nc, nerve cord;

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central nervous system - epidermis - tail muscles -

Transcription of a transgene containing an internal deletion of the region between nucleotide positions -1110 and -473 of Nru-Z was activated in muscle cells. In some embryos, trunk ventral cells were stained. mu, muscle; tvc, trunk ventral cells.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	tail muscles - trunk ventral cells (B7.5 line) -

Deletion analyses revealed that 1,326 bp of the 5 prime flanking region of Ci-RAR was sufficient for driving the lacZ expression in the CNS, epidermis, and muscle, where endogenous Ci-RAR gene expression was observed. br, brain; ep, epidermis; mu, muscle;

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central nervous system - epidermis - tail muscles -

Deletion analyses revealed that 1,326 bp of the 5 prime flanking region of Ci-RAR was sufficient for driving the lacZ expression in the CNS, epidermis, and muscle, where endogenous Ci-RAR gene expression was observed. br, brain; ep, epidermis; mu, muscle; nc, nerve cord; me, mesenchyme;

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central nervous system - epidermis - tail muscles -

Deletion analyses revealed that 1326 bp of the 5 prime flanking region was sufficient for driving the lacZ expression in the CNS, epidermis, and muscle, where endogenous Ci-RAR gene expression was observed. However, the 1113-Z expression in the epidermis was restricted to the dorsal midline region. br,brain; ep, epidermis; mu, muscle; nc, nerve cord;

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central nervous system - central ventral head epidermis (a7.12 line) - dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - tail muscles -

Lateral view of a tailbud embryo electroporated with Ci-RAR cis-regulatory region in which region from -735 to -218 was deleted, upstream a LacZ reporter gene.

This deletion doesn't seem to affect the expression. The reporter expression was detected in the DME (Dorsal Midline Epidermis), the head endoderm, the nerve cord (NC), and in the brain (BR).

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central nervous system - dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - head endoderm -

Lateral view of a tailbud embryo electroporated with Ci-RAR cis-regulatory region in which region from -863 to -218 was deleted, upstream a LacZ reporter gene (DME, Dorsal Midline Epidermis ; VME, Ventral Midline Epidermis).

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central nervous system - dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - head endoderm - tail muscles - ventral head epidermis -

Lateral view of a tailbud embryo electroporated with the Ci-RAR cis-regulatory region in which region from 953 to -218 was deleted, upstream a LacZ reporter gene (DME, dorsal midline epidermis ; NC, nerve cord, VME, ventral midline epidermis, BR, brain).

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central nervous system - dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - head endoderm - tail muscles - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis -

Transgenes containing 548 bp or 287 bp of the 5 prime flanking region were expressed in muscle cells. In some experiments, a small number of embryos expressed these transgenes in the CNS. br, brain; mu, muscle; me, mesenchyme;

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central nervous system - tail muscles -

Expression of the transgene containing 814 bp of the 5 prime flanking region (814-Z) was almost completely missing in the entire epidermis. 814-Z was expressed in the brain, nerve cord, and muscle. br, brain; nc, nerve cord; mu, muscle; me, mesenchyme;

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central nervous system - tail muscles - trunk lateral cells (A7.6 line) -

Embryo electroporated with Ci-RAR cis-regulatory region in which region from -1016 to -218 was deleted, upstream a LacZ reporter gene. (construct named delta5-Z in the paper)

Original annotation:
The expression of LacZ was not detected when Delta5-Z was introduced.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	No expression -

Lateral view of a tailbud embryo electroporated with Ci-RAR cis-regulatory region in which region from -987 to -218 was deleted, upstream a LacZ reporter gene (construct named delta4-Z in the paper).

Original annotation:
The expression of lacZ was not detected when Delta4-Z was introduced.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	No expression -

Transgenes containing 548 bp or 287 bp of the 5 prime flanking region were expressed in muscle cells. Two E-boxes were found within 287 bp of the 5 prime flanking sequence. Mutation in one of them (E1: CACGTG) did not affect the transgene expression in the muscle. In contrast, mutation in the other (E2: CAACTG) diminished the expression.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	tail muscles -

Transgenes containing 548 bp or 287 bp of the 5 prime flanking region were expressed in muscle cells. Two E-boxes were found within 287 bp of the 5 prime flanking sequence. Mutation in one of them (E1: CACGTG) did not affect the transgene expression in the muscle. In contrast, mutation in the other (E2: CAACTG) diminished the expression.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	tail muscles -

Transgenes containing 287 bp of the 5 prime flanking region were expressed in muscle cells (br, brain; mu, muscle).

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central nervous system - tail muscles -

Lateral view of a tailbud embryo electroporated with Ci-RAR cis-regulatory region in which region from -962 to -218 was deleted, upstream a LacZ reporter gene (construct named MA1-Z in the paper). The most anterior region of the DME derived from the a8.26 blastomere pairs is indicated by a blue bracket.

Original Annotation : The expression of lacZ was observed in the dorsal midline epidermis (DME) when MA1-Z was introduced. A small fraction of transgenic embryos showed weak expression in the neural tube, tail muscle and ventral midline epidermis (NC, nerve cord).

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	anterior sensory vesicle - dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - tail muscles - tail nerve cord - ventral head epidermis -

Views of early tailbud stage showing reporter expression of the region upstream of Ci-RAR from -697bp to -394bp in muscle, mesenchyme and a part of brain.

Aniseed Annotation : According to the pictures, the brain staining is very weak and only detected in few embryos.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	posterior sensory vesicle - tail muscles -

A transgene containing 4,037 bp of the 5 prime flanking region, named Ci-RAR/lacZ, was expressed in the CNS, epidermis, and muscle, where endogenous Ci-RAR gene expression was observed. Three examples are shown depicting the expression pattern of Ci-RAR/lacZ that contains 4,037 bp of the 5 prime flanking region. br, brain; ep, epidermis; mu, muscle; nc, nerve cord; no, notochord.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	central nervous system - epidermis - notochord - tail muscles -

Lateral view of a tailbud embryo electroporated with Ci-RAR cis-regulatory region in which region from -953 to -218 and region from -1002 to -986 were deleted, upstream a LacZ reporter gene (construct named MB1-Z in the paper).

Original annotation:
Electroporation of MB1-Z resulted in the expression only in the tail muscle cells (MU). No expression was observed in the dorsal midline epidermis (DME).

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	tail muscles -

Embryos probed for the reporter expression of the region upstream of Ci-RAR from -1113bp to 0bp. In this construction (named MB2-Z in the paper) a region from -1017 to -986 and an other from -953 to -218 were deleted.

These deletions result in a loss of reporter expression in the DME (Dorsal Midline Epidermis). There is expression in tail muscles (MU), in mesenchyme (MC), and weak expression in brain.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	anterior sensory vesicle - tail muscles -

Lateral view of a tailbud embryo electroporated with Ci-RAR cis-regulatory region in which region from -953 to -218 and region from -1047/-986 were deleted, upstream a LacZ reporter gene (named MB4-Z in the paper).

Original annotation:
Electroporation of MB3-Z did not result in the expression of lacZ in the dorsal midline epidermis (DME). In this case, the expression of lacZ was observed in some other tissues (MC, mesenchyme).

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	tail muscles -

Lateral view of a tailbud embryo electroporated with Ci-RAR cis-regulatory region in which region from -953 to -218 and region from -1032 to -986 were deleted, upstream a LacZ reporter gene.

Original annotation:
Electroporation of MB3-Z did not result in the expression of lacZ in the dorsal midline epidermis (DME). In this case, the expression of lacZ was observed in some other tissues (BR, brain).

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	anterior sensory vesicle - neck - posterior sensory vesicle - tail muscles - visceral ganglion -

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :RAR.
Expression pattern : nervous system, nerve cord, endoderm, muscle.
Comment : The expression in muscle cells was weak. Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.

Aniseed annotation : staining posterior to the brain might have been localized in part of the posterior sensory vesicle and/or in part of the neck and/or in part of the visceral ganglion.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	head endoderm - neck - posterior sensory vesicle - tail muscles - tail nerve cord - visceral ganglion -

Views of mid tailbud stage embryos showing reporter expression of the region upstream of RAR in the posterior sensory vesicle and in a part of mesenchyme.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	posterior sensory vesicle -

Views of mid tailbud stage embryos showing reporter expression of the region upstream of RAR in mesenchyme and notochord.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	notochord -

Views of larvae showing reporter expression of the region upstream of RAR drived by Brachyury in mesenchyme and notochord.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	notochord -

Views of larvae embryos showing reporter expression of the region upstream of RAR in brain and mesenchyme.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	anterior sensory vesicle - neck - posterior sensory vesicle - visceral ganglion -

Views of larvae showing reporter expression of the region upstream of RAR in muscle, mesenchyme and a part of brain.

Stained molecule	KH2012:KH.C9.580 (RARA; RARB; RARG)
Stained region(s)	posterior sensory vesicle - tail muscles -