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 :E(spl)/hairy-b.
Expression pattern : Unlocalized signal was detected.
Comment : Maternal signal was observed ubiquitously mainly in the early claeving stages.

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 :E(spl)/hairy-b.
Expression pattern : No distinct zygotic signal was detected.
Comment : Maternal signal was observed ubiquitously mainly in the early claeving stages.

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 :E(spl)/hairy-b.
Expression pattern : A6.1, A6.2, A6.3, A6.4, B6.1, B6.4.
Comment : Maternal signal was observed ubiquitously mainly in the early claeving stages.

Vegetal view of a WT Ciona robusta late 32-cell stage embryo probed for E(Spl)/hairy-b expression.
Expression is observed in A-line, B6.1, B6.2 and B6.4 blastomere pairs.
In schematic representation of gene expression, notochord and nerve cord precursors mother cells are in purple. Blastomeres with gene expression are marked by dots.

Vegetal view of a late 32-cell stage embryo. The hybridization signal of E(spl)/hairy-b gene was weakly detected in nuclei of vegetal blastomeres.

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 :E(spl)/hairy-b.
Expression pattern : No distinct zygotic signal was detected

Vegetal view of a WT Ciona robusta 64-cell stage embryo probed for E(Spl)/hairy-b expression.
Expression is observed in A7.1, A7.2, A7.3, A7.5, A7.7, B7.1, B7.2 and B7.3 blastomere pairs.
In schematic representation of gene expression, notochord precursors are shown in red. Blastomeres with gene expression are marked by dots.

Early gastrula stage embryo probed for Ci-Hesb expression. No picture available in the article.

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 :E(spl)/hairy-b.
Expression pattern : A8.16, B8.6

Vegetal view of a 110-cell stage wild type embryo probed for Ci-Hes-b expression.

Original annotation: Ci-Hes-b is expressed in the A8.16 (neural/muscle fate) A8.14 (primary notochord) and B8.6 (secondary notochord).

Aniseed annotation: according to the picture, weak expression might have detected in A7.6 cell pair.

Vegetal view of a WT Ciona robusta 112-cell stage embryo probed for E(Spl)/hairy-b expression.
Expression is observed in A8.16, b8.19, B8.5, B8.6, B8.7 and B8.8 blastomere pairs.
In schematic representation of gene expression, notochord precursors are shown in red. Blastomeres with gene expression are marked by dots.

Vegetal view of a late gastrula stage wild type embryo probed for E(spl)/hairy-b expression.

Original Annotation :
E(spl)/hairy-b was expressed in A9.15, A9.16, A9.29, A9.30 and A9.32 cell pairs in the neural plate.

Neural plate view of a Mid gastrula stage wild type embryo probed for Ci-HES-b expression. Expression is detected in A9.39, A9.30, A9.29, a9.49, a9.33.

Vegetal view of a mid gastrula stage wild type embryo probed for Ci-Hesb expression.

Original Annotation : Ci-Hesb expression is detected in part of neural plate and in A9.31 cell pairs.

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

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 :E(spl)/hairy-b.
Expression pattern : nervous system, epidermis

Neural plate view of a late gastrula stage wild type embryo probed for Ci-HES-b expression. Expression is detected in A9.29, A9.30 and a9.33.

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 :E(spl)/hairy-b.
Expression pattern : nervous system, epidermis

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

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 :E(spl)/hairy-b.
Expression pattern : nervous system, epidermis.
Comment : The expression in the brain is discontinuous. The staining from the tail to the trunk is observed in a pair of lines of epidermal cells.

Lateral view of the motor ganglion of a WT Ciona robusta early tailbud embryo probed for HesB expression (green) and electroporated with FGF8/17/18>mCherry reporter construct (red).
HesB is expressed in A11.119 motor neuron precursor (arrowhead).
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei).

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

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 :E(spl)/hairy-b.
Expression pattern : nervous system, epidermis.
Comment : The expression in the brain is discontinuous. The staining from the tail to the trunk is observed in a pair of lines of epidermal cells.

Picture 1: ventral view of tail epidermis of a mid tailbud stage wild type embryo stained with DAPI

Picture 2: lateral view of a mid tailbud stage wild type embryo probed for Hesb expression.

Lateral view of the motor ganglion of a WT Ciona robusta mid tailbud embryo probed for Ngn (red) and HesB (green) expressions and electroporated with FGF8/17/18>H2B:CFP reporter construct (blue nuclei).
Original comment: At the mid-tailbud stage, Ngn expression (red) has refined to presumptive neurons A12.239, A13.474, A11.118 and A11.117. This alternates with HesB expression (green), in accordance with general models of lateral inhibition, except in A11.118/A11.117 pair (asterisks).
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (blue nuclei).

Lateral view of the motor ganglion of a WT Ciona robusta mid tailbud embryo probed for Ngn (red) and HesB (green) expressions and electroporated with FGF8/17/18>H2B:CFP reporter construct (blue nuclei).
Original comment: At the mid-tailbud stage, Ngn expression (red) has refined to presumptive neurons A12.239, A13.474, A11.118 and A11.117. This alternates with HesB expression (green), in accordance with general models of lateral inhibition, except in A11.118/A11.117 pair (asterisks).
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (blue nuclei).

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

In situ hybridization was conducted on young animals (1–1.5 months old;2–3mminlength) grown in culture (Jeffery,2015b)
"We detected hes-b expression in body wall muscle and the stigmatal cells of the branchial sac"
BS: transverse vessels in the branchial sac. Arrows in B, F indicate mRNA localization in the branchial sac transverse vessels (B) or stigmata (F)

Ciona intestinalis young adults probed for Hairy-b expression.
Hairy-b is expressed in the branchial basket (bb). In the oral siphon (os), at the base of the tentacles (t), the label is at the tunic level.
(as) is for atrial syphon.
Original comment: We observed Hairy-b expression at the level of the pharyngeal gills. Stained cells were located at the two extremities of the elliptical stigmata, where an undifferentiated population of cells, giving rise to the ciliated cells is present.
Scale bars: 200 μm

Figure C : Control (unoperated animals)
OPO: oral siphon pigment