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.

Unfertilized Ciona robusta egg probed for Ci-Dll-B expression. Dll-B expression is observed.

Conversion to Aniseed format of data from Yutaka Satous gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Dll-B.
Expression pattern : Pem-like localized signal was detected.
Comment : 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-Dll-B maternal transcript : Pem localized signal was detected.

8-cell stage wild type Ciona robusta embryo probed for Ci-Dll-B expression.
Dll-B is expressed in B4.1 blastomer pair.
No picture available for this stage.

Localization or distribution pattern of Ci-Dll-B (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.

Conversion to Aniseed format of data from Yutaka Satous gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Dll-B.
Expression pattern : No distinct zygotic signal was detected.
Comment : The expression in the posterior end/endodermal strand is maternal.

Conversion to Aniseed format of data from Yutaka Satous gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Dll-B.
Expression pattern : No distinct zygotic signal was detected.
Comment : The expression in the posterior end/endodermal strand is maternal.

64-cell wild type embryo probed for Dll-B expression (picture 1: animal pole view, picture 2: vegetal pole view, picture 3: posterior view with animal pole up showing staining in all animal hemisphere cells, picture 4: vegetal pole view, showing DAPI counterstaining).

Original annotation : transcripts are detected in all a-line and b-line blastomeres of the animal hemisphere. No detectable expression is seen in any vegetal blastomeres except for strong signal in the two small contralateral B7.6 cells (arrowhead).

Conversion to Aniseed format of data from Yutaka Satous gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Dll-B.
Expression pattern : a7.9, a7.10, a7.11, a7.12, a7.13, a7.14, a7.15, a7.16, b7.9, b7.10, b7.11, b7.12, b7.13, b7.14, b7.15, b7.16.
Comment : The expression in the posterior end/endodermal strand is maternal.

Conversion to Aniseed format of data from Yutaka Satous gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Dll-B.
Expression pattern : a8.17, a8.18, a8.19, a8.20, a8.21, a8.22, a8.23, a8.24, a8.25, a8.26, a8.27, a8.28, a8.29, a8.30, a8.31, a8.32, b8.17, b8.18, b8.19, b8.20, b8.21, b8.22, b8.23, b8.24, b8.25, b8.26, b8.27, b8.28, b8.29, b8.30, b8.31, b8.32.
Comment : The expression in the posterior end/endodermal strand is maternal.

Vegetal and animal views of an early gastrula wild type embryo probed for Dll-B expression.

Original Annotation :
Expression was detected in a line, B7.6 cell pair and b line.

Original Annotation : Views of early gastrula stage embryos showing reporter expression of the region upstream of Dll-B in a-line and b-line cells. Signal in neural precursors were weaker.

Ci-DB-1.0 transgenic embryos. Picture 1 : diagram of the DB-1.0 transgene constructs. Non-coding sequence is represented by red bars aligned with corresponding sequence in Vista plot above. LacZ reporter gene insertion is represented by a blue bar. Extent of expression of each transgene in reporter experiments is shown at right as percentages of aggregate anterior and posterior animal quadrants with staining for beta-galactosidase.

(G) Animal and (H) vegetal pole views at early gastrula stage. Cells in H which appear on the vegetal side (arrowhead) are b8.17 and b8.19 cells derived from the animal hemisphere.

Ventral view of a WT Ciona robusta gastrula stage embryo probed for Ci-Dll-B expression.
Dll-B expression is observed in one cell of the B7.6 lineage (arrow).

Dorsal view of a WT Ciona robusta gastrula stage embryo probed for Ci-Dll-B expression.
Dll-B is expressed in the epidermis and in the neural plate.

Ci-DB-2.4 transgenic embryos. Picture 1 : diagram of the DB-2.4 transgene constructs. Non-coding sequence is represented by red bars aligned with corresponding sequence in Vista plot above. LacZ reporter gene insertion is represented by a blue bar. Extent of expression of each transgene in reporter experiments is shown at right as percentages of aggregate anterior and posterior animal quadrants with staining for beta-galactosidase.
(B) Representative animal pole views of transgenic embryos.

Original annotation:
However, the reporter with 5 kb of upstream sequence (CiDB-5.0) was able to drive expression in a higher proportion of animal hemisphere cells, like the whole-cluster construct, than a shorter construct lacking 5 short segments of conserved sequence (CiDB-2.4; Fig. 3B).

Ci-DB-1.5 transgenic embryos. Picture 1 : diagram of the DB-1.5 transgene constructs. Non-coding sequence is represented by red bars aligned with corresponding sequence in Vista plot above. LacZ reporter gene insertion is represented by a blue bar. Extent of expression of each transgene in reporter experiments is shown at right as percentages of aggregate anterior and posterior animal quadrants with staining for beta-galactosidase.
(C) Representative animal pole views of transgenic embryos.

Original annotation:
Interestingly, eliminating the next conserved segment (B2 in Fig. 1A) (CiDB-1.5; Fig. 3C), increases the extent of expression, suggesting that B2 is an attenuator.

Ci-DB-0.2 transgenic embryos. Picture 1 : diagram of the DB-0.2 transgene constructs. Non-coding sequence is represented by red bars aligned with corresponding sequence in Vista plot above. LacZ reporter gene insertion is represented by a blue bar. Extent of expression of each transgene in reporter experiments is shown at right as percentages of aggregate anterior and posterior animal quadrants with staining for beta-galactosidase.
(E) Representative animal pole views of transgenic embryos.

Original annotation:
A reporter gene with only 200 bp of upstream sequence (CiDB-0.2; Fig. 3E) showed no lacZ signal.

Diagrams of reporter transgenes associated with the B1 conserved sequence element. Representation of the position of the B1 CNS within the CiDB-1.0 construct (top). Predicted transcription factor binding sites are shown by colored ovals. Below are diagrams of CiDB-1.0d10 reporter transgene construct. Chart at right shows the extent of expression of each transgene as percentages of aggregate number of anterior and posterior animal quadrants with staining for beta-galactosidase.

Original annotation:
Deletion of the entire 378 bp conserved B1 sequence (construct CiDB-1.0d10; Fig. 4) completely obliterates reporter gene expression.

Diagrams of reporter transgenes associated with the B1 conserved sequence element. Representation of the position of the B1 CNS within the CiDB-1.0 construct (top). Predicted transcription factor binding sites are shown by colored ovals. Below are diagrams of CiDB-1.0d4 reporter transgene construct. Chart at right shows the extent of expression of each transgene as percentages of aggregate number of anterior and posterior animal quadrants with staining for beta-galactosidase.
(A) Reporter transgene expression - B1 region analysis. Representative animal pole views of transgenic embryos.

Original annotation:
Even with relatively large deletions from proximal part of B1(CiDB-1.0d4), expression in all four animal quadrants is maintained.

Diagrams of reporter transgenes associated with the B1 conserved sequence element. Representation of the position of the B1 CNS within the CiDB-1.0 construct (top). Predicted transcription factor binding sites are shown by colored ovals. Below are diagrams of CiDB-1.0d7 reporter transgene construct. Chart at right shows the extent of expression of each transgene as percentages of aggregate number of anterior and posterior animal quadrants with staining for beta-galactosidase.

Representation of the position of the B1 CNS within the CiDB-1.0 construct (top). Predicted transcription factor binding sites are shown by colored ovals. Below is diagram CiDB-0.2-0.44 reporter transgene construct.Chart at right shows the extent of expression of each transgene as percentages of aggregate number of anterior and posterior animal quadrants with staining for beta-galactosidase.
(D) Reporter transgene expression - B1 region analysis. Representative animal pole views of transgenic embryos.

Original annotation:
(C) 440 bp upstream of Ci-Dll-B drives expression only in the posterior animal hemisphere, similar to that seen when the proximal 211 bp of B1 is tested upstream of a heterologous Ci-FoxA-a promoter (D).

Representation of the position of the B1 CNS within the CiDB-1.0 construct (top). Predicted transcription factor binding sites are shown by colored ovals. Below is diagram CiDB-0.35-0.62 reporter transgene construct.Chart at right shows the extent of expression of each transgene as percentages of aggregate number of anterior and posterior animal quadrants with staining for beta-galactosidase.
(E) Reporter transgene expression - B1 region analysis. Representative animal pole views of transgenic embryos.

Original annotation:
The more distal 276 bp of B1 is able to drive expression in all quadrants of the animal hemisphere, upstream the stronger Ci-FoxA-a promoter (E).

Representation of the position of the B1 CNS within the CiDB-1.0 construct (top). Predicted transcription factor binding sites are shown by colored ovals. Below is diagram CiDB-p0.35-0.5 reporter transgene construct.Chart at right shows the extent of expression of each transgene as percentages of aggregate number of anterior and posterior animal quadrants with staining for beta-galactosidase.
(H) Reporter transgene expression - B1 region analysis. Representative animal pole views of transgenic embryos.

Original annotation:
Another short fragment, CiDBp-0.35-0.5 (Fig. 5H) also drives posterior expression, in this case with only a low level of anterior (a-line) quadrants staining.

Diagrams of reporter transgenes associated with the B1 conserved sequence element. Representation of the position of the B1 CNS within the CiDB-1.0 construct (top). Predicted transcription factor binding sites are shown by colored ovals. Below is diagram of CiDB-1.0d5 reporter transgene construct. Chart at right shows the extent of expression of each transgene as percentages of aggregate number of anterior and posterior animal quadrants with staining for beta-galactosidase.
(B) Reporter transgene expression - B1 region analysis. Representative animal pole views of transgenic embryos.

Original annotation:
Even with relatively large deletions from distal part of B1 (CiDB-1.0d5), expression in all four animal quadrants is maintained.

Late gastrula stage wild type embryo probed for Dll-B expression (picture 1: animal view; picture 2: vegetal view; picture 3: vegetal view showing DAPI counterstaining).

Original annotation : note staining in animal hemisphere cells that are moving over the vegetal side by epiboly. By mid-gastrula stage, expression in the most animal (ventral) ectoderm drops off, with strong expression retained in the animal side of the equatorial zone, and in the anterior neural plate.

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

Conversion to Aniseed format of data from Yutaka Satous gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Dll-B.
Expression pattern : epidermis.
Comment : The expression in the posterior end/endodermal strand is maternal.

Views of late gastrula stage embryos showing reporter expression of the region upstream of Dll-B in a-line and b-line cells.

Ci-DB-5.0 transgenic embryos. Picture 1 : diagram of the DB-5.0 transgene constructs. Non-coding sequence is represented by red bars aligned with corresponding sequence in Vista plot above. LacZ reporter gene insertion is represented by a blue bar. Extent of expression of each transgene in reporter experiments is shown at right as percentages of aggregate anterior and posterior animal quadrants with staining for beta-galactosidase.
(A) Representative animal pole views of transgenic embryos.

Original annotation:
The reporter with 5 kb of upstream sequence (CiDB-5.0; Fig. 3A) was able to drive expression in a higher proportion of animal hemisphere cells, like the whole-cluster construct.

Representation of the position of the B1 CNS within the CiDB-1.0 construct (top). Predicted transcription factor binding sites are shown by colored ovals. Below is diagram CiDBp-0.35-0.62 reporter transgene construct.Chart at right shows the extent of expression of each transgene as percentages of aggregate number of anterior and posterior animal quadrants with staining for beta-galactosidase.
(G) Reporter transgene expression - B1 region analysis. Representative animal pole views of transgenic embryos.

Original annotation:
The more distal 276 bp of B1 is able to drive expression in all quadrants of the animal hemisphere upstream of the native Ci-Dll-B promoter.

Representation of the position of the B1 CNS within the CiDB-1.0 construct (top). Predicted transcription factor binding sites are shown by colored ovals. Below is diagram CiDB-0.35-0.62mG reporter transgene construct.Chart at right shows the extent of expression of each transgene as percentages of aggregate number of anterior and posterior animal quadrants with staining for beta-galactosidase.
(F) Reporter transgene expression - B1 region analysis. Representative animal pole views of transgenic embryos.

Original annotation:
Mutation of a canonical GATA site in this fragment reduces, but does not eliminate expression in the same domain.

Representation of the position of the B1 CNS within the CiDB-1.0 construct (top). Predicted transcription factor binding sites are shown by colored ovals. Below is diagram CiDB-0.44 reporter transgene construct.Chart at right shows the extent of expression of each transgene as percentages of aggregate number of anterior and posterior animal quadrants with staining for beta-galactosidase.
(C) Reporter transgene expression - B1 region analysis. Representative animal pole views of transgenic embryos.

Original annotation:
440 bp upstream of Ci-Dll-B drives expression only in the posterior animal hemisphere.

Early neurula stage wild type embryo probed for Dll-B expression (picture 1: lateral view; picture 2: dorsal view; picture 3: dorsal view showing DAPI counterstaining).

Original annotation : by neurula stage the overall staining of ectoderm abruptly disappears, only being retained in a few cells of the anterior neuroectoderm. At the earlier neurula stage examined here four cells of the anterior neural plate are stained (arrowhead).

Aniseed annotation : according to the pictures, it seems that the staining is localised in a9.36 and a9.40 cell pairs.

Conversion to Aniseed format of data from Yutaka Satous gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Dll-B.
Expression pattern : nervous system, epidermis.
Comment : The expression in the posterior end/endodermal strand is maternal.

Mid neurula stage wild type embryo probed for Dll-B expression (picture 1: dorsal view showing DAPI counterstaining; picture 2: dorsal view; picture 3: lateral view).

Original annotation : expression has been partitioned to two bilateral patches of two cells each at the same apparent anteroposterior level (arrowhead).

Aniseed annotation : according to the pictures, it seems that the staining is localised in a10.71 and a10.72 cell pairs (precursors of palps).

Lateral view of a WT Ciona robusta early tailbud stage embryo probed for Ci-Dll-B expression.
There is a positive signal in two cells of the endodermal strand (es).

Dorsal view of an early tailbud stage wild type embryo probed for Dll-B expression.

Original annotation : the location of the cells stained (arrows) is consistent with an identity as precursors of the palps. However no signal was detected at later stages where palp development is visible.

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

Conversion to Aniseed format of data from Yutaka Satous gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Dll-B.
Expression pattern : nervous system, epidermis.
Comment : palp, ventral epidermis near the neck region, the expression in the endodermal strand is maternal.

Lateral view of a WT Ciona robusta middle tailbud stage embryo probed for Ci-Dll-B expression. There is a positive signal in one cell of the endodermal strand (es).

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

Conversion to Aniseed format of data from Yutaka Satous gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Dll-B.
Expression pattern : No distinct zygotic signal was detected.
Comment : the expression in the endodermal strand is maternal

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

Conversion to Aniseed format of data from Yutaka Satous gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Dll-B.
Expression pattern : No distinct zygotic signal was detected.
Comment : the expression in the endodermal strand is maternal.

Views of late tailbud stage embryos showing reporter expression of the region upstream of Dll-B in a-line and b-line cells.

Views of larvae showing reporter expression of the region upstream of Dll-B in a-line and b-line cells.