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 data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :TTF1.
Expression pattern : No signal was detected

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

Original annotation :
Gene name :TTF1.
Expression pattern : No distinct zygotic signal was detected

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

Original annotation :
Gene name :TTF1.
Expression pattern : No distinct zygotic signal was detected

Vegetal view of a WT Ciona robusta probed for Nkx2-1 expression at the 64-cell stage.
Original comment: Nkx2-1 was expressed in the vegetal blastomeres designated A7.1, A7.2, A7.5, B7.1, and B7.2 at the 64-cell stage.

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

Original annotation :
Gene name :TTF1.
Expression pattern : A7.1, A7.2, A7.5, B7.1, B7.2

Vegetal view of a 110-cell stage wild type embryo probed for TTF1 expression.

Original annotation :
Gene name :TTF1.
Expression pattern : A7.1, A7.2, A7.5, B7.1, B7.2

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

Original annotation :
Gene name :TTF1.
Expression pattern : A7.1, A7.2, A7.5, B7.1, B7.2

Vegetal view of a 110-cell stage embryo showing expression of TTF-1 in endoderm cell pairs.

Vegetal view of a WT Ciona robusta early gastrula stage embryo probed for Titf expression.
Titf is expressed in A7.1, A7.2, A7.5, B7.1 and B7.2 blastomer pairs.

Vegetal view of a WT Ciona robusta early gastrula stage embryo probed for Titf expression.
Titf, an endoderm marker, is expressed in B7.1, B7.2, A7.1, A7.2 and A7.5 blastomere pairs.

Vegetal and lateral view of an early gastrula stage embryo stained with TTF1 expression. Red arrow point to the NN cells, blue arrow point to the E cell.
(+HD photo)
Original annotation: Expression not observed in NN cells. No expression in animal view.
Aniseed annotation: Expression also observed in B7.1 and B7.2.

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

Original annotation :
Gene name :TTF1.
Expression pattern : No distinct zygotic signal was detected

No expression is observed.

No expression is observed.

Neurula stage embryo, electroporated with a LacZ transgene that contains the -3,5kb of the 5' flanking Cititf1 enhancer sequence. Staining is observed exclusively in cells of the endoderm lineage.

Be careful, coordinates of the regulatory region in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates in the paper : -3500bp/+238bp

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

Original annotation :
Gene name :TTF1.
Expression pattern : No distinct zygotic signal was detected

Lateral view of a late-neurula stage embryo, electroporated with a LacZ transgene that contains the region from -553bp of the 5' flanking Cititf1 enhancer sequence (construct #5E in the paper). Staining is observed exclusively in cells of the endoderm lineage.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -355bp/+238bp

Lateral view of a late-neurula stage embryo, electroporated with a LacZ transgene that contains the region from -350bp to +39bp of the 5' flanking Cititf1 enhancer sequence (construct #6 in the paper). Staining was lost from the endodermal cells, while a signal was visible in an ectopic territory corresponding to mesenchyme cells.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -152bp/+238bp

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

Original annotation :
Gene name :TTF1.
Expression pattern : No distinct zygotic signal was detected

Lateral and dorsal views of an early tailbud stage embryo, showing expression of ci-NKX21. Expression of ci-NKX21 was detected by whole-mount in situ hybridization.

Tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -3,5 kb of the 5' flanking Cititf1 enhancer sequence (construct #1 in the paper). Staining is observed exclusively in cells of the endoderm lineage. No picture available for in the paper.

Be careful, coordinates of the regulatory region in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates in the paper : -3500bp/+238bp

Tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -2,5 kb to of the 5' flanking Cititf1 enhancer sequence (construct #7 in the paper). Staining is observed exclusively in cells of the endoderm lineage. No picture available for in the paper.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -2370bp/+238bp

Tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -1058bp of the 5' flanking Cititf1 enhancer sequence (construct #3E in the paper). Staining is observed exclusively in cells of the endoderm lineage. No picture available for in the paper.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -860bp/+238bp

Tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -946bp of the 5' flanking Cititf1 enhancer sequence (construct #3 in the paper). Staining is observed exclusively in cells of the endoderm lineage. No picture available for in the paper.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -748bp/+238bp

Tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -724bp to of the 5' flanking Cititf1 enhancer sequence (construct #4 in the paper). Staining is observed exclusively in cells of the endoderm lineage. No picture available for in the paper.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -526bp/+238bp

Lateral view of an early tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -553bp of the 5' flanking Cititf1 enhancer sequence (construct #5E in the paper). Staining is observed exclusively in cells of the endoderm lineage.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -355bp/+238bp

Tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -263bp of the 5' flanking Cititf1 enhancer sequence (construct #10E in the paper). No picture available for in the paper.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -65bp/+238bp

Tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -1114bp the 5' flanking Cititf1 enhancer sequence (construct #2 in the paper). Staining is observed exclusively in cells of the endoderm lineage. No picture available for in the paper.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -916bp/+238bp

Control : Lateral view of a early-tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -553bp of the 5' flanking Cititf1 enhancer sequence. Staining is observed exclusively in cells of the endoderm lineage.

Picture 1 : Lateral view of a early-tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -553bp of the 5' flanking Cititf1 enhancer sequence which contains a mutation: attcttatttGCATTTGATTTccgttc -> attcttatttTACGGGTCGGCccgttc (construct S2m3 in the paper). Staining is lost

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -355bp/+238bp

Tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -553bp of the 5' flanking Cititf1 enhancer sequence (construct #5E/10E/6 in the paper). Staining is observed exclusively in cells of the endoderm lineage. No picture available for in the paper.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -355bp/+238bp

Tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -553bp to -239bp of the 5' flanking Cititf1 enhancer sequence (construct #0.2-5E/10E in the paper). Staining is observed exclusively in cells of the endoderm lineage. No picture available for in the paper.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -355bp/+238bp

Tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -553bp to -328bp of the 5' flanking Cititf1 enhancer sequence (construct delta4 in the paper). Staining is observed exclusively in cells of the endoderm lineage. No picture available for in the paper.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -355bp/-130bp

Tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -553bp to -399bp of the 5' flanking Cititf1 enhancer sequence (construct delta3 in the paper). No picture available for in the paper.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -355bp/-201bp

Tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -553bp to -519bp of the 5' flanking Cititf1 enhancer sequence (construct delta1 in the paper). No picture available for in the paper.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -355bp/-321bp

Picture 1 : Lateral view of a early-tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -481bp to +39bp of the 5' flanking Cititf1 enhancer sequence (construct #1E in the paper). Staining is observed exclusively in cells of the endoderm lineage.

Picture 2 : Ventral view of a early-tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -481bp to +39bp of the 5' flanking Cititf1 enhancer sequence. Staining was evident in cells of the endoderm lineage.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -283bp/+238bp
Name of the construct in the paper : construct delta1 #1E

Lateral and ventral view of a early-tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -433bp to +39bp of the 5' flanking Cititf1 enhancer sequence (construct #2E in the paper). Staining is observed in endoderm cells but 10% in addition showed betagalactosidase activity in the mesenchymal cells of the trunk (indicated by arrow).

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -235bp/+238bp

Lateral view of a early-tailbud stage embryo, electroporated with a LacZ transgene that contains the region from -350bp to +39bp of the 5' flanking Cititf1 enhancer sequence (construct #6 in the paper). Staining was lost from the endodermal cells, while a signal was visible in an ectopic territory corresponding to mesenchyme cells.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -152bp/+238bp

Views of early tailbud stage embryos showing reporter expression of the region upstream of Ci-COE in mesenchyme and in muscle.

Lateral and dorsal views of a mid tailbud wild type embryos probed for Ci-Nkx2.1. These pictures show expression in two ventrolateral bands in the posterior sensory vesicle.

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 :TTF1.
Expression pattern : nervous system, endoderm.
Comment : brain and endoderm

Tadpole stage embryo, electroporated with a LacZ transgene that contains the -3,5kb of the 5' flanking Cititf1 enhancer sequence. Staining is observed in the anterior/ventral endoderm of the trunk.

Be careful, coordinates of the regulatory region in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates in the paper : -3500bp/+238bp

Lateral view of a tadpole stage embryo, electroporated with a LacZ transgene that contains the region from -553bp of the 5' flanking Cititf1 enhancer sequence (construct #5E in the paper). Staining is observed exclusively in cells of the endoderm lineage.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -355bp/+238bp

Control : Lateral view of a tadpole stage embryo, electroporated with a LacZ transgene that contains the region from -553bp of the 5' flanking Cititf1 enhancer sequence (construct #5E in the paper). Staining is observed exclusively in cells of the endoderm lineage.

Picture 1 : Lateral view of a tadpole stage embryo, electroporated with a LacZ transgene that contains the region from -553bp of the 5' flanking Cititf1 enhancer sequence which contains mutations by transversion of the nucleotides GCGCT in position -464bp to -460bp (construct M12 in the paper). This electroporation showed a decrease of the endodermal expression.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -355bp/+238bp

Control : Lateral view of a tadpole stage embryo, electroporated with a LacZ transgene that contains the region from -553bp of the 5' flanking Cititf1 enhancer sequence. Staining is observed exclusively in cells of the endoderm lineage.

Picture 1 : Lateral view of a tadpole stage embryo, electroporated with a LacZ transgene that contains the region from -553bp of the 5' flanking Cititf1 enhancer sequence which contains mutations by transversion of the nucleotides TTTGC in position -411bp to -407bp (construct M19 in the paper). This electroporation showed a decrease of the endodermal expression.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -355bp/+238bp

Lateral view of a tadpole stage embryo, electroporated with a LacZ transgene that contains the region from -350bp to +39bp of the 5' flanking Cititf1 enhancer sequence (construct #6 in the paper). Staining was lost from the endodermal cells, while a signal was visible in an ectopic territory corresponding to mesenchyme cells.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -152bp/+238bp

Control : Lateral view of a tadpole stage embryo, electroporated with a LacZ transgene that contains the region from -553bp to +39bp of the 5' flanking Cititf1 enhancer sequence. Staining is observed exclusively in cells of the endoderm lineage.

Picture 1 : Lateral view of a tadpole stage embryo, electroporated with a LacZ transgene that contains the region from -553bp to +39bp of the 5' flanking Cititf1 enhancer sequence which contains mutations by transversion of the nucleotides TGATT in position -403bp to -399bp (construct M20 in the paper). This electroporation showed a decrease of the endodermal expression.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates of this region in the paper : -355bp/+238bp

Views of larvae showing reporter expression of the region upstream of Ci-COE from -1043bp to -480bp in mesenchyme and in muscle.