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.

Original annotation:
Pem localized signal was detected. The expression in the posterior end/endodermal strand is maternal.

Fertilized eggs just after the second phase of ooplasmic segregation viewed from lateral side. Localization or distribution pattern of Ci-RhoGAP-a maternal transcript : Pem localized signal was detected.

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal.

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

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal.

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

Localization or distribution pattern of Ci-RhoGAP-a(which is a maternal transcript) in 8-cell stage embryos, revealed by whole-mount in situ hybridization. Embryos viewed from the right side and from the posterior side. Pem localized signal was detected in B4.1 cell pair.

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal.

Aniseed annotation:
Pem localized signal was detected in B5.2 cell pair. Expression is also detected through the whole embryo.

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal.

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

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal.

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

64-cell stage wild type embryo probed for ciad19a17 clone. Expression was detected in the notochord from the initial tailbud stage (data not shown in the article).

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal.

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

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal.

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-RhoGAP-a is redistributed only into B8.11 cells. Expression is also detected through the whole embryo.

Mid gastrula stage wild type embryo probed for ciad19a17 clone. Expression was detected in the notochord from the initial tailbud stage (data not shown in the article).

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal.

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-RhoGAP-a is redistributed only into B8.11 cells. Expression is also detected through the whole embryo.

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal.

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-RhoGAP-a is redistributed only into B8.11 cells. Expression is also detected through the whole embryo.

Mid neurula stage wild type embryo probed for ciad19a17 clone. Expression was detected in the notochord from the initial tailbud stage (data not shown in the article).

Initial tailbud wild type embryo probed for ciad19a17 clone. Expression was detected in the notochord from the initial tailbud stage (data not shown in the article).

Original annotation:
Staining is observed in the notochord. The expression in the posterior end/endodermal strand is maternal.

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-RhoGAP-a is redistributed only into B8.11 cells. Expression is also detected through the whole embryo.

Original annotation:
Staining is observed in the notochord. The expression in the posterior end/endodermal strand is maternal.

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-RhoGAP-a is redistributed only into B8.11 cells. Expression is also detected through the whole embryo.

Mid tailbud wild type embryo probed for ciad19a17 clone. Expression was detected in the notochord from the initial tailbud stage (data not shown in the article).