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 Ghost database entry from Nishikata T et al., Dev Biol. 2001; 238:315-331. Original annotation: weak. Expression pattern: Localized

Conversion to Aniseed format of data from Miwata et al. (2006) Dev Biol. 292(2)
Original annotation: Although signals of pem-like distribution were detected from 8-cell stage stage, clear localized signals were not observed in fertilized egg. Gene: Ci-ZF118. Expression pattern: expressed and unlocalized.

View of a 2-cell stage embryo. Localization of Ci-DEAD1 mRNA during embryogenesis. Whole-mount in situ hybridization was performed with Ci-DEAD1 antisense probe.

View of a 4-cell stage embryo. Localization of Ci-DEAD1 mRNA during embryogenesis. Whole-mount in situ hybridization was performed with Ci-DEAD1 antisense probe.

Original annotation: during the second cleavage, however, a part of the transcript moved to the posterior region of the embryo, and then this signal was localized subcellularly in the posterior region of B3 blastomeres at the 4-cell stage (arrowheads).

Aniseed annotation: Pem localized signal was detected in B3 cell pair. Staining is also detected through the whole embryo.

Conversion to Aniseed format of Ghost database entry from Nishikata T et al., Dev Biol. 2001; 238:315-331. Original annotation: . Expression pattern: A4.1 a4.2 B4.1 b4.2

View of a 8-cell stage embryo. Localization of Ci-DEAD1 mRNA during embryogenesis. Whole-mount in situ hybridization was performed with Ci-DEAD1 antisense probe.

Original annotation: as embryogenesis proceeded, the transcript was inherited by the posterior-most blastomeres: B4.1 blastomeres at the 8-cell stage.

Aniseed annotation: Pem localized signal was detected in B4.1 cell pair. Weak expression is also detected through the whole embryo.

Conversion to Aniseed format of data from Miwata et al. (2006) Dev Biol. 292(2)
Original annotation: pem-like distribution Gene: Ci-ZF118. Expression pattern: no distinct zygotic signal was detected.

Conversion to Aniseed format of data from Miwata et al. (2006) Dev Biol. 292(2)
Original annotation: pem-like distribution Gene: Ci-ZF118. Expression pattern: no distinct zygotic signal was detected.

Animal view of a 16-cell stage embryo. Localization of Ci-DEAD1 mRNA during embryogenesis. Whole-mount in situ hybridization was performed with Ci-DEAD1 antisense probe.

Original annotation: as embryogenesis proceeded, the transcript was inherited by the posterior-most blastomeres.

Aniseed annotation: Pem localized signal was detected in B6.3 cell pair. Expression is also detected through the whole embryo.

Conversion to Aniseed format of data from Miwata et al. (2006) Dev Biol. 292(2)
Original annotation: pem-like distribution Gene: Ci-ZF118. Expression pattern: no distinct zygotic signal was detected.

Vegetal view of a 64-cell stage embryo. Localization of Ci-DEAD1 mRNA during embryogenesis. Whole-mount in situ hybridization was performed with Ci-DEAD1 antisense probe.

Original annotation: As embryogenesis proceeded, the transcript was inherited by the posterior-most blastomeres.

Aniseed annotation: Pem localized signal was detected in B7.6 cell pair. Expression is also detected through the whole embryo.

Conversion to Aniseed format of data from Miwata et al. (2006) Dev Biol. 292(2)
Original annotation: pem-like distribution Gene: Ci-ZF118. Expression pattern: no distinct zygotic signal was detected.

Vegetative view of an early gastrula stage embryo. Localization of Ci-DEAD1 mRNA during embryogenesis. Whole-mount in situ hybridization was performed with Ci-DEAD1 antisense probe.

Original annotation: As embryogenesis proceeded, this transcript was inherited by the posterior-most blastomeres: B7.6 at the 110-cell stage.

Aniseed annotation: Pem localized signal was detected in B7.6 cell pair. Expression is also detected through the whole embryo.

Conversion to Aniseed format of data from Miwata et al. (2006) Dev Biol. 292(2)
Original annotation: pem-like distribution Gene: Ci-ZF118. Expression pattern: no distinct zygotic signal was detected.

Conversion to Aniseed format of data from Miwata et al. (2006) Dev Biol. 292(2)
Original annotation: pem-like distribution Gene: Ci-ZF118. Expression pattern: no distinct zygotic signal was detected.

View of a mid neurula stage embryo. Localization of Ci-DEAD1 mRNA during embryogenesis. Whole-mount in situ hybridization was performed with Ci-DEAD1 antisense probe.

Original annotation: at the neurula stage two clusters of hybridization signal were seen posteriorly along the midline of the embryo.

Aniseed annotation: posterior blastomeres B7.6 cells produce two daughter cells names B8.11 and B8.12 cells (Shirae-Kurabayashi et al., in press). Ci-DEAD1 is redistributed into B8.12 cells in addition to B8.11 cells. Expression is also detected in the mesenchyme, the epidermis and in the nervous system.

Conversion to Aniseed format of data from Miwata et al. (2006) Dev Biol. 292(2)
Original annotation: In additiion pem-like maternal expression, zygotic signals were detected in endoderm, a part of endodermal strand, brain, nerve cord. Gene: Ci-ZF118. Expression pattern: endodermal strand.

View of an early tailbud stage embryo. Localization of Ci-DEAD1 mRNA during embryogenesis. Whole-mount in situ hybridization was performed with Ci-DEAD1 antisense probe.

Original annotation: the signal in the posterior cluster (arrowhead) was weaker than that of the anterior one (arrow).

Aniseed annotation: posterior blastomeres B7.6 cells produce two daughter cells names B8.11 and B8.12 cells (Shirae-Kurabayashi et al., in press). Ci-DEAD1 is redistributed into B8.12 cells in addition to B8.11 cells. Expression is also detected in the mesenchyme, the trunk epidermis, head endoderm and in the nervous system.

A mid tailbud wild type embryo probed for Ci-VH antisens riboprobe.

Original Annotation : Strong signal is detected in the anterior neural tube (nt) and the endoderm regions (en), as well as in a few endodermal strand cells (es and arrowheads).
nc means notochord.

A mid tailbud wild type embryo probed for Ci-VH thanks to an immunostaining.

Original Annotation : Strong signal is detected in the anterior neural tube and the endoderm regions (en), as well as in a few endodermal strand cells (es and arrowheads) in the tail.
mu means muscle.

View of a mid tailbud stage embryo. Localization of Ci-DEAD1 mRNA during embryogenesis. Whole-mount in situ hybridization was performed with Ci-DEAD1 antisense probe.

Original annotation: the signal in the posterior cluster (arrow) was weaker than that of the anterior one, and this signal disappeared by the middle tailbud stage.

Aniseed annotation: posterior blastomeres B7.6 cells produce two daughter cells names B8.11 and B8.12 cells (Shirae-Kurabayashi et al., in press). Ci-DEAD1 is expressed only in B8.11 cells from this stage. Expression is also detected in the mesenchyme, the trunk epidermis, head endoderm and in the nervous system.

Conversion to Aniseed format of data from Miwata et al. (2006) Dev Biol. 292(2)
Original annotation: In additiion pem-like maternal expression, zygotic signals were detected in endoderm, endodermal strand, brain, a part of nerve cord, mesenchyme and epidermis in trunk. Gene: Ci-ZF118. Expression pattern: endodermal strand.

View of a late tailbud stage embryo. Localization of Ci-DEAD1 mRNA during embryogenesis. Whole-mount in situ hybridization was performed with Ci-DEAD1 antisense probe.

Original annotation: the signal in the posterior cluster (arrow) was weaker than that of the anterior one, and this signal disappeared by the middle tailbud stage.

Aniseed annotation: posterior blastomeres B7.6 cells produce two daughter cells names B8.11 and B8.12 cells (Shirae-Kurabayashi et al., in press). Ci-DEAD1 is expressed in to B8.11 cells from mid tailbud stage. Expression is also detected in the mesenchyme, the trunk epidermis, head endoderm and in the nervous system.

Views of a tadpole wild type embryo probed for Ci-VH thanks to an immunostaining. The second picture is a magnified view of the area boxed in the first picture.

Original Annotation : Expression was detected in the endodermal strand of the posterior half of the tail. (arrowheads in the second picture).
"nc" means notochord.

Views of a tadpole wild type embryo probed for Ci-VH thanks to an immunostaining. The first picture is a tail cut larva, the second a removed larval tail and the last a magnifient view of the area boxed in the second picture.

Original Annotation : Expression was detected in the endodermal strand of the posterior half of the tail. (arrowheads in the second picture).

Left side view of a young adult probed for Ci-DEAD1 expression.

Original Annotation : In the largest animals the vesicular structure (show previously ISH 3232183 and 3232184) divides distinctly into two parts. One part has a large lumen in which one large stained cell exists as in B (arrowhead). Another part looks heart-shaped and many smaller stained cells aggregate in its right wall margin (arrow).

Left side view of a young adult probed for Ci-DEAD1 expression.

Original Annotation : In this young adult we can see in its distal part (left) there is a lumen in which one large stained cells exists, its proximal part (right) contains many smaller stained cells, from which thin tubular structure extends above along the intestine (arrowhead). This tube seems to be a gonoduct.

Left side view of a young adult probed for Ci-DEAD1 expression.

Original Annotation : Hybridization signals are found in several large oval cells in the vesicular structure (arrowhead) located in the space between intestine (IN) and esophagus (ES). This vesicular structure seems to be a gonad rudiment.

Views of an adult wild type probed for Ci-VH thanks to an immunostaining.

Original Annotation : Expression was detected in the debris of the larval tail (d and arrowheads) and also next to the stomach(st) and the pyloric gland (pg) in the last picture.

Views of an adult wild type probed for Ci-VH thanks to an immunostaining. The first picture is a view of ovary and the second of testis.

Original Annotation : In the ovary, the signal is distributed throughout the cytoplasm of smaller oocytes and in the perinuclear cytoplasm of larger oocytes.
In the testis, large spermatogenous cells localized in the peripheral region of tubulus seminiferus were strongly stained by the antibody, while sperm (sp) was not.

Views of gonad of an adult wild type probed for Ci-VH thanks to an immunostaining. Pic H is counter-stained with eosin Y.

Original Annotation : G and H are sections at the level indicated by a red line in E.
In the pics A, B and C we can see expression in the future gonad (gr, gonad rudiment) (arrowheads) near to the pyloric gland (pg). Perhaps there is staining in the peritoneum of the intestine (in)(arrowheads in C) and also in stomach (st) (pics D, E). Stained cells are also present in the testis (pic F) containing the mature sperm (sp) (G, H)
"gr" means gonad rudiment, "in" intestine, "oo" oocyte, "ov" ovary, "pg" pyloric gland, "sp" sperm, "st" stomach, "ts" testis.

Views of sections of an adult wild type probed for Ci-VH thanks to an immunostaining. The pictures were taken at different times (9 day old : D, 15-day-old : E, 32-day-old : F, 53-day-old : G).

Original Annotation : Ci-VH was expressed at this stage in intestine (in, black arrowheads) in the future gonad (white arrowhead) and in the space between the stomach (st) and the esophagus (pics D/E).