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: . Expression pattern: not detected

Original annotation:
Pem localized signal was detected. The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression was detected.

Zygote embryo probed for cieg002j02 (no picture available in the paper).

Original annotation: maternal transcript was detected as both pem-like signal that localized at the posterior and unlocalized signal.

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

Aniseed Annotation:
Pem localized signal was detected in B3 cell pair. Weak expression is 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: pem-like. Expression pattern: B4.1 Pem-like expression

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

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

Characteristic expression patterns of the positive genes detected by whole-mount in situ hybridization. Posterior view of a 8-cell stage embryo, showing expression of cieg002j02.

Original annotation: maternal transcript was detected as both pem-like signal that localized at the posterior and unlocalized signal.

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

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

Characteristic expression patterns of the positive genes detected by whole-mount in situ hybridization. Vegetal view of a 16-cell stage embryo, showing expression of cieg002j02.

Original annotation: at the 16-cell stage, the signal became strong in all cells.

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

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

32-cell stage embryo probed for cieg002j02 (no picture available in the paper).

Original annotation: all cells.

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

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

Characteristic expression patterns of the positive genes detected by whole-mount in situ hybridization. Vegetal view of a 64-cell stage embryo, showing expression of cieg002j02.

Original annotation: expression remained in the muscle precursors and neural tube precursors that were located along the margin of the animal and vegetal hemisphere at the 64- and 110-cell stage.

Aniseed annotation: muscle precursors at 64-cell stage are A7.8, B7.4, B7.5, B7.8 and b7.9 cell pairs; neural tube precursors are A7.4, A7.8 and b7.10 cell pairs at 64-cell stage.

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

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

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

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-pem7 is redistributed into B8.12 cells in addition to B8.11 cells. Weak staining is also detected through the whole embryo.

Characteristic expression patterns of the positive genes detected by whole-mount in situ hybridization. Vegetal view of a late gastrula stage embryo, showing expression of cieg002j02.

Original annotation: Expression is localized in cells around the blastopore at the gastrula stage.

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

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-pem7 is redistributed into B8.12 cells in addition to B8.11 cells. Weak staining is also detected through the whole embryo.

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

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-pem7 is redistributed into B8.12 cells in addition to B8.11 cells.

Neurula stage embryo probed for cieg002j02 (no picture available in the paper).

Original annotation: no distinct zygotic signal detected.

Original annotation:
No zygotic signal was detected. The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

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-pem7 is redistributed into B8.12 cells in addition to B8.11 cells.