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 :DMRT1.
Expression pattern : Unlocalized 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 :DMRT1.
Expression pattern : No distinct zygotic signal was detected.
Comment : Weak ubiquitous staining (maybe maternal expression) was observed mainly in the early cleaving stages.

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 :DMRT1.
Expression pattern : No distinct zygotic signal was detected.
Comment : Weak ubiquitous staining (maybe maternal expression) was observed mainly in the early cleaving stages.

Anterior (left) and animal (right) views of a WT Ciona robusta probed for Dmrt1 expression at the early 32-cell stage.
Original comment: We detected a weak signal in the anterior animal cells (a6.5) at the 32-cell stage of normal embryos.

Animal (left) and anterior (right) views of a Ciona robusta 32-cell stage embryo electroporated with the Dmrt1(-486bp)>LacZ reporter construct.
Scale bar, 100 μm.
LacZ signal is observed in the a6.5 blastomer pair.
Original comment: The construct containing the 486-bp upstream sequence of Dmrt1 showed almost the same activity as the endogenous gene.

Animal (left) and anterior (right) views of a Ciona robusta embryo at the early 32-cell stage electroporated with the Dmrt1 -486+µFoxd>LacZ construct. LacZ signal is observed in the A6.2, A6.4 and a6.5 cell pairs.
Original comment: The mutant upstream sequence drove reporter expression in the vegetal hemisphere, suggesting that Foxd directly represses Dmrt1 expression via this site.

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 :DMRT1.
Expression pattern : No distinct zygotic signal was detected.
Comment : Weak ubiquitous staining (maybe maternal expression) was observed mainly in the early cleaving stages.

Animal view of a Ciona robusta 64-cell stage embryo probed for Dmrt1 expression and injected with a control morpholino oligo.
Dmrt1 expression is observed in a7.9, a7.10 and a7.13 blastomers.
n, number of embryos examined. % : Percentages of embryos with Foxa.a expression in the neural lineage (cyan arrowheads).

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 :DMRT1.
Expression pattern : a7.9, a7.10, a7.13.
Comment : Weak ubiquitous staining (maybe maternal expression) was observed mainly in the early cleaving stages.

An animal view of a 64 cells stage wild type embryo probed for DMRT1 expression. Original annotation :
Expression was detected is a7.9, a7.10, a7.13. Original Comment :
Weak ubiquitous staining (maybe maternal expression) was observed mainly in the early cleaving stages.

Views of 64-cell stage embryos showing weak reporter expression of the region upstream of DMRT1 in a7.9 and a7.10 cells.

Views of 64-cell stage embryos showing weak reporter expression of the region upstream of DMRT1 in a7.9 and a7.10 cells.

Original annotation :
Gene name :DMRT1.
Expression pattern : a8.17, a8.18, a8.19, a8.20, a8.25, a8.26

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 :DMRT1.
Expression pattern : a8.17, a8.18, a8.19, a8.20, a8.25, a8.26

Animal view with anterior to the top of a 112-cell stage embryo (stage 10) stained with Dmrt1. In the panel, anterior ectoderm in white, posterior ectoderm in yellow and gene expression in blue. Expression was observed in the a8.17, a8.18, a8.19, a8.20, a8.25 and a8.26 cell pairs.

Views of early gastrula stage embryos showing weak reporter expression of the region upstream of DMRT1 in a8.17, a8.18, a8.19 and a8.20 cells.

Views of early gastrula stage embryos showing weak reporter expression of the region upstream of DMRT1 in a8.17, a8.18, a8.19 and a8.20 cells.

Animal view of a Ciona robusta early gastrula stage embryo probed for Dmrt1 expression and injected with a control morpholino oligo.
Dmrt1 expression is observed in a8.17, a8.18, a8.19, a8.20, a8.25 and a8.26 cell pairs.
n, number of embryos examined. % : Percentages of embryos with Foxa.a expression in the neural lineage (cyan arrowheads).

View of a mid-gastrula stage embryo stained with DMRT by a DMRT>lacZ transgene detected by β-gal antibony (red) and hoechst for DNA.
Expression is observed in a-line cells (row III to VI) originating from the a7.10 and a7.9 cell pairs at the 64-cell stage.
The left-right mosaicism is due to the electroporation of plasmids.

View of rows III-VI of a mid-gastrula embryo labeled with DMRT>GFP (green) in the presence of a LacZ control driven by the DMRT enhancer.
DMRT expression was observed in rows III and IV.

View of rows III-VI of a mid-gastrula embryo labeled with DMRT>β-gal (red) antibody as well as hoechst for DNA (blue) in DMSO control. DMRT expression was observed in rows III and IV.

View of rows III-VI of a mid-gastrula embryo labeled with DMRT>GFP(green) in the presence of a LacZ control driven by the DMRT enhancer. DMRT expression was observed in rows III and IV.

View of rows III-VI of a mid-gastrula embryo labeled with DMRT>β-gal antibody (red) as well as hoechst for DNA (blue) in DMSO control. DMRT expression was observed in rows III and IV.

View of rows III-VI of a mid-gastrula embryo labeled with DMRT>β-gal (green) antibody as well as hoechst for DNA (blue) in DMSO control. DMRT expression was observed in rows III and IV.

View of rows III-VI of a mid-gastrula embryo labeled with DMRT>β-gal (green) antibody as well as hoechst for DNA (blue) in DMSO control. DMRT expression was observed in rows III and IV.

View of rows III-VI of a mid-gastrula embryo labeled with DMRT>β-gal (green) antibody as well as hoechst for DNA (blue) in DMSO control. DMRT expression was observed in rows III and IV.

View of rows III-VI of a mid-gastrula embryo labeled with DMRT>β-gal (green) antibody as well as hoechst for DNA (blue) in DMSO control. DMRT expression was observed in rows III and IV.

View of rows III-VI of a mid-gastrula embryo labeled with DMRT>GFP (green) in the presence of a LacZ control driven by the DMRT enhancer. DMRT expression was observed in rows III and IV.

View of rows III-VI of a mid-gastrula embryo labeled with DMRT>β-gal (red) antibody as well as hoechst for DNA (blue) in the presence of a LacZ control driven by the DMRT enhancer. DMRT expression was observed in rows III and IV.

View of rows III-VI of a mid-gastrula embryo labeled with DMRT>GFP (green) with a FoxC minimal enhancer fragment containing two Ets binding sites cloned upstream of a heterologous promoter (from the FOG gene) driving LacZ . DMRT expression was observed in rows III and IV.

Vegetal view of a mid gastrula WT embryo co-electroporated with Dmrt>H2B:CFP (blue, nuclei) and ZicL>mCherry:caax (magenta, plasma membrane).
Original annotation : Rows V and VI express Dmrt exclusively and contribute to the palps, OSP, and peripheral nervous system. ZicL and Dmrt reporters co-localize in rows III and IV, which give rise to the anterior sensory vesicle. Rows I and II express ZicL exclusively and contribute to posterior brain, motor ganglion, and tail nerve cord. Scale bars in (C, D)1⁄450 μm.

Vegetal view of a mid gastrula WT embryo probed for Six3/6 expression (red) and electroporated with Dmrt>LacZ (white). LacZ signal is observed in a-line neural plate.

Vegetal view of a mid gastrula WT embryo probed for Myt1L (red) and Tyrp1A (green) expression and electroporated with Dmrt>LacZ (white). LacZ signal is observed in a-line neural plate.

Vegetal view of a mid gastrula embryo probed for Six3/6 expression (red) and co-electroporated with Dmrt>H2B:YFP (green) and ZicL>LacZ (white). YFP is detected in a-neural plate.

Vegetal view of a mid gastrula embryo probed for Elk1/3/4 expression (red), co-electroporated with Dmrt>YFP:caax (green) and ZicL>LacZ (white).
Membrane-targeted YFP is detected in a-line 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 Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :DMRT1.
Expression pattern : nervous system

Aniseed annotation :
ubiquitous staining is observed through the embryo.

Views of late gastrula stage embryos showing weak reporter expression of the region upstream of DMRT1 in a-line neural plate cells.

Vegetal view of a late gastrula embryo probed for Ets1/2 expression (red), co-electroporated with Dmrt>YFP:caax (green) and ZicL>LacZ (white).
Membrane-targeted YFP is detected in a-line 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 Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :DMRT1.
Expression pattern : nervous system

Vegetal view of a late gastrula embryo probed for Ets1/2 expression (red), co-electroporated with Dmrt>YFP:caax (green) and ZicL>LacZ (white).
Membrane-targeted YFP is detected in a-line neural plate.

Original annotation : Dorsal view of an initial tailbud embryo co-electroporated with Six1/2GFP (green) and ZicL>CFP (yellow). Brackets indicate the derivatives of the annotated lineages. Anterior is to the left.
DMRT enhancer drives GFP expression throughout the anterior neural plate and adjacent anterior ectoderm.

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 :DMRT1.
Expression pattern : nervous system
Comment : brain
Aniseed comment: Update to follow the original comments

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 :DMRT1.
Expression pattern : nervous system
Comment : brain.

Views of mid tailbud stage embryos showing reporter expression of the region upstream of DMRT1 in palps and brain. Expression was also detected ectopically in muscle, notochord and mesenchyme.

Views of mid tailbud stage embryos showing reporter expression of the region upstream of DMRT1 in palps and brain. Expression was detected ectopically in muscle, notochord and mesenchyme. Some weak expression in the neck and the visceral ganglion was detected in few embryos.

View of a tailbud stage embryo labeled with DMRT>H2B:CFP (blue) in the presence of a LacZ control driven by the DMRT enhancer. Yellow dotted line indicates the brain vesicle and embryo outline.
DMRT expression was observed in anterior brain cells (pink cells: co-expression of DMRT and ZicL) as well as in the anterior trunk ectoderm (palp placode and progeny of a9.51 and a9.52).

View of a tailbud stage embryo labeled with DMRT>mCherry (red) and phalloidin staining (green/actin marker)in the presence of a LacZ control driven by the DMRT enhancer. Yellow dotted line indicates the brain vesicle outline and the asterisk indicates the neuropore.
DMRT expression was observed in anterior brain cells (pink cells: co-expression of DMRT and ZicL) as well as in the anterior trunk ectoderm (palp placode and progeny of a9.51 and a9.52).

Dmrt regulatory sequence drives GFP expression throughout the anterior neural plate and adjacent anterior ectoderm.
Original annotation: These experiments were performed using a previously described Dmrt regulatory DNA (that is, Dmrt.GFP), which drives expression throughout the anterior neural plate and adjacent anterior ectoderm (row IV, row V and row VI neural plate).
Aniseed annotation: fates corresponding to row IV, V and VI neural plate and to the picture are anterior sensory vesicle, neurohypophysis primordium, palps, RTEN, siphon primordia

Lateral view of a late tailbud embryo co-electroporated with Dmrt>H2B:CFP (blue, nuclei) and ZicL>mCherry:caax (magenta, plasma membrane).
Original annotation : Colored linesindicate territories derived from neural plate rows. Rows V and VI express Dmrt exclusively and contribute to the palps, OSP, and peripheral nervous system. ZicL and Dmrt reporters co-localize in rows III and IV, which give rise to the anterior sensory vesicle. Rows I and II express ZicL exclusively and contribute to posterior brain, motor ganglion, and tail nerve cord. Scale bar 1⁄450 μm.

View of a tailbud stage embryo stained with DMRT driving β-gal (green/DMRT>β-gal) in DMSO control. The yellow bracket indicates the anterior brain. Expression was observed in the anterior brain as well as a leaky expression in the tail muscles and notochord.

Views of larvae showing reporter expression of the region upstream of DMRT1 in palp and brain. Expression was also detected ectopically in muscle, notochord and mesenchyme. Few embryos expressed the reporter in the neck and the visceral ganglion, but expression was weak.

Views of larvae embryos showing reporter expression of the region upstream of DMRT1 in palps and brain. Expression was detected ectopically in muscle, notochord and mesenchyme. According to the pictures, expression in the mesenchyme was weak and present in few embryos only.

Original annotation : Larva electroporated with DMRT>Cherry-caax (Red) and FoxC>H2B:CFP (Blue) to label anterior neural plate and palp lineage, respectively. Control larva expressing DMRT>lacZ and FoxC>lacZ shows normal palp development.

Lateral view of a larvae co-electroporated with Dmrt>H2B:mCherry (magenta) and Arrestin>H2B:CFP (blue).
Original annotation : Clusters of Arrestin cells are consistently observed posterior to the Dmrt expression domain.
Dmrt reporter is observed in the sensory vesicle and in the palps, but not in the photoreceptors.

Conversion to Aniseed format of Ghost database entry from Ogasawara et al., Dev Genes Evol. 2002; 212:173-185. Original annotation: . Expression pattern: not detected