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.

64-cell stage wild type embryo probed for Ci-fibrn expression. Expression was detected from the late gastrula stage.

110-cell stage wild type embryo probed for Ci-fibrn expression. Expression was detected from the late gastrula stage.

Mid gastrula stage wild type embryo probed for Ci-fibrn expression. Expression was detected from the late gastrula stage.

Neural plate view of a Late gastrula stage wild type embryo probed for Ci-fibrn expression. Expression was detected from the late gastrula stage.

Neural plate view of a Mid neurula stage wild type embryo probed for Ci-fibrn expression. Expression was detected from the late gastrula stage.

Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: . Expression pattern: Notochord

Dorsal view of a initial tailbud stage wild type embryo probed for Ci-fibrn expression. Expression was detected from the late gastrula stage.

Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: . Expression pattern: Notochord

Whole-mount in situ hybridization showing the gene expression profile specific to organs and/or tissues in Ciona intestinalis tailbud embryos. Cluster 00347, encoding a fibrinogen-like protein, is expressed in a notochord-specific manner.

Lateral view of a WT Ciona robusta early tailbud embryo probed for Fgl expression.
Fgl expression is observed in the notochord.
This control embryo was injected with a control MO into the pair of anterior animal cells at the 8-cell stage.
n, number of embryos examined. % : percentage of embryos with ectopic expression.

Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: epidermis in the tail. Expression pattern: Notochord Epidermis

Lateral view of a mid tailbud stage wild type embryo probed for a gene that encodes a component of the ECM, a prothrombinase precursor. In situ hybridization assays revel localized expression of the gene in the notochord.

Lateral view of a Mid tailbud stage wild type embryo probed for Ci-fibrn expression. Expression was detected from the late gastrula stage.

Activity of the region upstream of Ci-fibrn from -3016bp to +38bp, in front of a LacZ reporter.

Original Annotation :
The p(-3.0 k)fibrn/lacZ construct exhibited notochord specific expression of the reporter gene.

Region upstream of Ci-fibrn from -3016bp to +38bp, in front of a LacZ reporter. A deletion from -875bp to -2781bp was performed. The construct was named p(-3.0 k (delta 2.7-0.8))fibrn/lacZ in the paper.

Original Annotation :
This construct was not able to drive notochord-specific expression of lacZ. Mesenchyme cells expressed the LacZ reporter.

Acitvity of a region upstream of Ci-fibrn from -3016bp to +38bp in front of a LacZ reporter. A deletion from -243bp to -908bp was performed. The construct was named p(-3.0 k (delta 1.0-0.2))fibrn/lacZ in the paper.

Original Annotation :
This construct was able to drive notochord-specific expression of lacZ.
According to the paper, ectopic expression was detected in mesenchyme.

Region upstream of Ci-fibrn from -2515bp to +38bp, in front of a LacZ reporter. The construct was named p(-2.5k)fibrn/lacZ in the paper.

Original Annotation :
The p(-2.5k)fibrn/lacZ construct exhibited notochord specific expression.