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.

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 :Hox3.
Expression pattern : No signal was detected

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 :Hox3.
Expression pattern : No distinct zygotic signal was detected

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 :Hox3.
Expression pattern : No distinct zygotic signal was detected

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 :Hox3.
Expression pattern : No distinct zygotic signal was detected

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 :Hox3.
Expression pattern : No distinct zygotic signal was detected

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 :Hox3.
Expression pattern : No distinct zygotic signal was detected

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 :Hox3.
Expression pattern : No distinct zygotic signal was detected

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 :Hox3.
Expression pattern : No distinct zygotic signal was detected

Lateral view of a tadpole stage embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -4,2kb to the first +174 bp (pHox3 -4200/+174::LacZ construct, construct named 4.2 in the paper). Staining is observed in the anterior region of the developing nervous system. ans; anterior nervous system.

Lateral view of a tadpole stage embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -450bp to the first +174bp (construct named 0.45 in the paper). The staining is lost in the nervous system and after 3-6 days,ectopic staining is observed in the mesenchymal pocket (mp).

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 :Hox3.
Expression pattern : No distinct zygotic signal was detected

Mid tailbud stage wild type embryo probed for Hox3 expression. No picture available in the article.

Original Annotation :
Hox3 expression was detected in A13.473 cell pair (visceral ganglion).

Lateral view of a late tailbud stage wild type embryo probed for Ci-Hox3 expression. This picture shows signal in the small region just behind the sensory vesicle (arrow) and also in the anterior tail epidermis (ep, epidermis).

The dashed line indicates the edge of the posterior pharyngeal endoderm. The dotted line indicates the region of the prospective stomach (n notochord, nc nerve cord, pe pharyngeal endoderm, ps prospective stomach, vg visceral ganglion).
Bar 50 μm (b), 20 μm (d).
Expression of Hox3 is mainly observed in the visceral ganglion; however strict expression is observed in the posterior pharyngeal endoderm

Lateral view of a tadpole stage wild type embryo probed for Ci-Hox3 expression. This picture shows expression in the visceral ganglion (vg, visceral ganglion).

Picture 1 and 2:
Lateral and dorsal view of a tadpole stage embryo hybridized with digoxigenin-labeled CiHox3 antisense RNA probe. Expression is detected in visceral ganglion (arrow).

Picture 3:
Transerversal section at the level of the visceral ganglion. Expression is observed in the most lateral external lateral cells of the ganglion.

Tadpole stage embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -180bp to the first +174bp (0.2 construct in the paper). Staining is lost .

Lateral view of a tadpole stage embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -4,2kb to the first +174 bp (pHox3 -4200/+175::LacZ construct, construct named 4.2 in the paper). Staining is observed in the visceral ganglion and ectopically in the sensory vesicle. sv; sensory vesicle, vg; visceral ganglion.

Embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -4,5kb to -3kb (pHox3 -4500/-3000::LacZ construct, construct named delta4-3 in the paper). Staining is observed ectopically in mesenchyme and disappear in nervous system. No picture available in the paper.

Embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -3kb to the first +174 bp (pHox3 -3000/+175::LacZ construct, construct named 3.0 in the paper). Staining is observed in the visceral ganglion and ectopically in the sensory vesicle. No picture available in the paper.

Embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -3kb to -2kb (pHox3 -3000/-2000::LacZ construct, construct named delta3-2 in the paper). Staining is observed ectopically in mesenchyme and disappear in nervous system. No picture available in the paper.

Embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -3kb to -2,5kb (pHox3 -3000/-2500::LacZ construct, construct named delta3-25 in the paper). Staining is observed ectopically in mesenchyme and disappear in nervous system. No picture available in the paper.

Embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -1.5b to the first +174 bp (pHox3 -1500/+175::LacZ construct, construct named 1.5 in the paper). Ectopic expression is observed in the mesenchyme. No picture available in the paper.

Embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -1kb to the first +174 bp (pHox3 -1000/+175::LacZ construct, construct named 1.0 in the paper). Ectopic expression is observed in the mesenchyme. No picture available in the paper.

Lateral view of a tadpole stage embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -450bp to the first +174bp (construct named 0.45 in the paper). The staining is lost in the nervous system and after 3-6 days ectopic expression is observed in the mesenchyme and trunk mesenchyme (tm).

Embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -2022bp to -1943bp (construct named P5 in the paper). Staining is observed in ectopically in mesenchyme. No picture available in the paper.

Embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -2022bp to -1862bp (construct named P4 in the paper). Staining is observed in sensory vesicle, visceral ganglion and ectopically in mesenchyme. No picture available in the paper.

Embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -1943bp to -1812bp (construct named P3 in the paper). Staining is observed in sensory vesicle, visceral ganglion and ectopically in mesenchyme. No picture available in the paper.

Embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -2022bp to -1507bp (construct named P1 in the paper). Staining is observed in sensory vesicle (sv), visceral ganglion (vg) and ectopically in mesenchyme.

Embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -1812bp to -1507bp (construct named P2 in the paper). Staining is ectopically in mesenchyme. No picture available in the paper.

Embryo electroporated with a construct that contains the CiHox3 cis-regulatory region from -1943bp to -1862bp (construct named P6 in the paper). Staining is observed in sensory vesicle (sv), visceral ganglion (vg) and ectopically in mesenchyme.

Conversion to Aniseed format of Ghost database entry from Ogasawara et al., Dev Genes Evol. 2002; 212:173-185. Original annotation: . Expression pattern: Endostyle Pharyngeal gill Neural gland Stomach Esophagus

Conversion to Aniseed format of Ghost database entry from Ogasawara et al., Dev Genes Evol. 2002; 212:173-185. Original annotation: . Expression pattern: Endostyle Neural gland

Young adult stage wild type embryo probed for Ci-Hox3 expression. This picture shows signal in the neural complex and in a part of the heart (nc, neural complex; ht, heart).

Expression signals were assessed by whole-mount in situ hybridization (WISH) and the NBT/BCIP coloring system under the stereomicroscope.
A. Representation of a 2– to 3-week-old Ciona juvenile, left side view (anterior, as atrial siphon, bs branchial sac, d dorsal, epc epicardium, endostyle, esp esophagus, int intestine, nc neural complex, os oral siphon, rpb retropharyngeal band, p posterior, pj protruding structures of the pharyngeal esophagus junction, st stomach, stg stigma, v ventral).
d. Hox3 expression in the ganglion of the posterior neural complex, posterior endostyle, epicardium, retropharyngeal band and the protruding structures of the pharyngeal esophagus junction. Bar 500 μm
“In 2– to 3-week-old juvenile specimens, the differential expression patterns of all genes in the ascidian Hox cluster were detected via a stereo microscope”

The blue stains (asterisks) in the stomach are nonspecific stains of intestinal inclusions (en endostyle, esp esophagus, int intestine, st stomach). Bars 100 μm
In the protruding structures of the pharyngeal esophagus junction (white arrowheads ventral side, gray arrowheads dorsal side, black arrowheads distal side), expression of Hox3 (g) is observed.
“In the endostyle, Hox3 (c) is expressed. For each gene, expression in the posterior region is stronger than the anterior region and the strongest signal was detected in the posterior terminus (white arrowheads).”

Expression domains are indicated by colored arrowheads: brown endostyle, purple esophagus, blue retropharyngeal band, green right epicardium, orange left side of left epicardium, red right side of left epicardium. Bar 100 μm
Expression was assessed from the left (a–d), right (e–h), anteroventral (i–l) and opposite views of the oral siphon (m–p). Expression was also assessed by using frontally sectioned specimens (q–t).
“Expression of Hox3 was detected in the retropharyngeal band and almost the entire region of the epicardium (Fig. 3c, g, k, o, s).”

Expression of Hox3 is also observed in the middle to posterior part of the cerebral ganglion, extending posterior to the neuron. Bar 20 μm.