27 results
| Library Name | Percentage | Expression |
|---|---|---|
| Ciona intestinalis whole animal Ciona intestinalis whole animal |
|
0 clone(s) / 0 |
| Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library |
|
0 clone(s) / 5,577 |
| Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult |
|
0 clone(s) / 31,366 |
| Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo |
|
0 clone(s) / 15,579 |
| Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg |
|
0 clone(s) / 31,100 |
| Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva |
|
0 clone(s) / 26,704 |
| Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo |
|
0 clone(s) / 26,680 |
| directional larval cDNA library directional larval cDNA library |
|
0 clone(s) / 39 |
| Ascidian hemocytes cDNA library Ascidian hemocytes cDNA library |
|
0 clone(s) / 0 |
| K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis |
|
0 clone(s) / 5,468 |
| Stratagene UniZAP whole-larva library Stratagene UniZAP whole-larva library |
|
0 clone(s) / 0 |
| Ciona intestinalis larva Ciona intestinalis larva |
|
0 clone(s) / 0 |
| Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells |
|
0 clone(s) / 29,579 |
| Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle |
|
0 clone(s) / 2,556 |
| Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo |
|
0 clone(s) / 16,939 |
| Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula |
|
0 clone(s) / 25,258 |
| Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad |
|
0 clone(s) / 16,936 |
| Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex |
|
0 clone(s) / 10,463 |
| Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart |
|
0 clone(s) / 13,243 |
| Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland |
|
0 clone(s) / 17,765 |
| Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal |
|
0 clone(s) / 17,872 |
| Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal |
|
0 clone(s) / 107,314 |
| Nori Satoh unpublished cDNA library, juvenile whole animal Nori Satoh unpublished cDNA library, juvenile whole animal |
|
0 clone(s) / 24,372 |
| Nori Satoh unpublished cDNA library, mature adult whole animal Nori Satoh unpublished cDNA library, mature adult whole animal |
|
0 clone(s) / 17,126 |
| Ciona intestinalis whole animal stage3 juvenile Ciona intestinalis whole animal stage3 juvenile |
|
0 clone(s) / 3,798 |
| Yutaka Satou unpublished library (cicx) Yutaka Satou unpublished library (cicx) |
|
0 clone(s) / 2,031 |
| Gateway compatible cien cDNA library, Ciona intestinalis mixed embryonic stages (Egg to Neurula) Gateway compatible cien cDNA library, Ciona intestinalis mixed embryonic stages (Egg to Neurula) |
|
0 clone(s) / 188,431 |
2 results
OVERVIEW
Click here to see the RNA-Seq Pipeline Protocol.
You can show/hide lines in the charts by clicking on it in the legend part.
You can see more details by clicking on a point and then, on the link which will appear.
Be careful, FPKM & RPKM does not permit you to compare a gene across different conditions or experiments.
OVERVIEW
Be careful, RLE and 2RLE does not permit you to compare a gene across different experiments.
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.
| Assay platform | Illumina HiSeq 2000 | |
| Layout | Paired-end | |
| Stranded | Yes | |
| Read length | 49 | |
| Normalized data types |
|
|
| Wild type - Replica 1 | ||
| Territories | whole embryo - | |
| Biomaterial(s) | C. robusta formely Ciona int. type A, Stage 0 (Unfertilized egg) | |
| C. robusta formely Ciona int. type A, Stage 8 (64-cell) | ||
| C. robusta formely Ciona int. type A, Stage 11 (early gastrula) | ||
| C. robusta formely Ciona int. type A, Stage 12 (mid gastrula) | ||
| C. robusta formely Ciona int. type A, Stage 15 (mid neurula) | ||
| C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I) | ||
| C. robusta formely Ciona int. type A, Stage 26 (hatching larva) | ||
| Wild type - Replica 2 | ||
| Territories | whole embryo - | |
| Biomaterial(s) | C. robusta formely Ciona int. type A, Stage 0 (Unfertilized egg) | |
| C. robusta formely Ciona int. type A, Stage 8 (64-cell) | ||
| C. robusta formely Ciona int. type A, Stage 11 (early gastrula) | ||
| C. robusta formely Ciona int. type A, Stage 12 (mid gastrula) | ||
| C. robusta formely Ciona int. type A, Stage 15 (mid neurula) | ||
| C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I) | ||
| C. robusta formely Ciona int. type A, Stage 26 (hatching larva) | ||
The purpose of this project is to identify genes positively and negatively regulated by signaling molecules that belongs to the TGFbeta superfamily.
| Assay platform | Illumina HiSeq 2500 | |
| Layout | Single-end | |
| Stranded | Yes | |
| Read length | 101 | |
| Normalized data types |
|
|
| Wild type | ||
| Territories | whole embryo - | |
| Biomaterial(s) | C. robusta formely Ciona int. type A, Stage 13 (late gastrula) | |
| Mutant 1 | ||
| Deregulated molecule(s) | KH2012:KH.C4.125 - | |
| Territories | whole embryo - | |
| Biomaterial(s) | C. robusta formely Ciona int. type A, Stage 13 (late gastrula) | |
| Mutant 2 | ||
| Deregulated molecule(s) | KH2012:KH.C2.573 - | |
| Territories | whole embryo - | |
| Biomaterial(s) | C. robusta formely Ciona int. type A, Stage 13 (late gastrula) | |
57 results
Lateral view of a 32-cell embryo probed for Ci-Dmbx expression. No expression was detected prior to the tailbud stage.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | No expression - |
Whole mount in situ hybridization of Ciona embryo showing Ci-Dmbx expression at neurula stage. No expression was detected prior to the tailbud stage.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | No expression - |
Dorsal view of a neurula stage embryo probed for Ci-Dmbx expression. No expression was detected prior to the tailbud stage.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | No expression - |
Whole mount in situ hybridization of Ciona embryo showing Ci-Dmbx expression at tailbud stage. Expression was first detected in one bilateral pair of cells in the neural tube.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Dorsal views of mid tailbud stage embryo expressing Dmbx. The upper panel shows WISH signals, the middle DAPI signals and the lower the merged images.
Arrowheads indicate nuclei of the cells that express Dmbx. Open arrows indicate the constrictions in the row of nuclei of the lateral cells. Red dots indicate nuclei of the landmark cells.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | lateral VG ependymal precursors - |
Comparison of Ci-Hox3 (blue stain) and Ci-Dmbx (red stain) at mid tail-bud stage embryo (lateral view), showing co-localised expression (arrowhead).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Dorsal view of mid tailbud stage embryo Sprobed for Ci-Dmbx. Expression is detected exclusively in the neural tube (precisely in one bilateral pair of cells).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | lateral VG ependymal precursors - |
Spatial and temporal expression of Ci-Dmbx at mid tailbud stage embryo deduced by whole-mount in situ hybridisation.
Original annotation : Ci-Dmbx expression is detected exclusively in the neural tube.(precisely in one bilateral pair of cells).
Aniseed annotation : according to the picture, it seems that the staining is localized in the visceral ganglion.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Comparison of expression between Ci-Dmbx (blue stain, arrowhead) and Ci-Pax2/5/8-A (red stain, arrow) at mid tailbud stage (lateral view).
Original Annotation: Ci-Dmbx is expressed in cells immediately posterior to cells expressing Ci-Pax2/5/8-A, with no gap and no overlap.
Aniseed Annotation: according to the pictures, it seems that the blue staining is localized in the visceral ganglion and the red staining in the neck.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | neck - visceral ganglion - |
Two-color fluorescence WISH was performed at the mid tailbud stage. Dmbx expression is shown in green, Fgf8/17/18 in red.
Original annotation:
Ci-Dmbx is expressed in part of visceral ganglion. The Ci-Dmbx domain did not overlap with the Ci-FGF8/17/18 domain.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Two-color-fluorescence WISH was performed at the mid tailbud stage. Dmbx expression is shown in red, En in green.
Original annotation:
Ci-Dmbx is expressed in part of the visceral ganglion. The Ci-Dmbx domain was located between the second and third domains of Ci-En at this stage.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Two-color fluorescence WISH was performed at the mid tailbud stage. Dmbx expression is shown in red, SoxB1 in green.
Original annotation:
Ci-Dmbx is expressed in part the of visceral ganglion. The Ci-Dmbx domain is located between these two expression domains of Ci-SoxB1.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Lateral view of a WT Ciona robusta mid tailbud embryo co-electroporated with Dmbx>GFP (green) and Msx>H2B:CFP (blue nuclei) reporter constructs.
GFP is observed in the motor ganglion. Asterisks indicate leaky Dmbx reporter expression in mesoderm.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | mesenchyme (B8.5 & B7.7 lines) - tail muscles - visceral ganglion - |
Lateral view of a WT Ciona robusta mid tailbud embryo co-electroporated with Dmbx>GFP (green) and Msx>H2B:CFP (blue nuclei) reporter constructs.
Msx reporter construct is active in the central nervous system, in the muscles precursors at the tip of the tail and in the tail epidermis.
| Stained molecule | KH2012:KH.C2.957 (DLX1; MSX1; MSX2) |
| Stained region(s) | central nervous system - dorsal midline anterior tail epidermis - dorsal midline posterior tail epidermis - secondary muscle lineage - tail epidermis - ventral midline posterior tail epidermis - |
Lateral view of a WT Ciona robusta mid tailbud embryo co-electroporated with Dmbx>GFP (green) and Msx>H2B:CFP (blue nuclei) reporter constructs and Msx>Ngn overexpression construct.
Msx reporter construct is active in the central nervous system, in the muscles precursors at the tip of the tail, in the tail epidermis.
| Stained molecule | KH2012:KH.C2.957 (DLX1; MSX1; MSX2) |
| Stained region(s) | central nervous system - tail epidermis - tail muscles - |
Lateral view of a WT Ciona robusta mid tailbud embryo co-electroporated with Dmbx>GFP (green) and Msx>H2B:CFP (blue nuclei) reporter constructs and Msx>Ngn overexpression construct.
Author's comment: Dmbx seems to be activated ectopically in some cells of the neural plate border (dorsal midline), but which cells remains unclear because of the developmental defects (which were prominent upon overexpression of Ngn there).
Asterisks indicate leaky Dmbx reporter expression in mesoderm.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | dorsal midline anterior tail epidermis - |
Data not shown at this developmental stage in the article.
Dmbx is expressed in A12.239 in WT Ciona rosusta mid tailbud stage embryos.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Lateral view of the motor ganglion of a Ciona robusta mid tailbud embryo probed for Dmbx expression (green) and electroporated with FGF8/17/18 reporter construct (red nuclei) and FGF8/17/18>Su(H)-DBM overexpression construct.
Original comment:Ectopic expression of A12.239 marker Dmbx in posterior daughter cell of A11.119 (A12.237, double arrowhead) upon inhibition of Notch signaling by FGF8/17/18>Su(H)-DBM (n=66/100). Single arrowhead indicates A12.239 cell.
The A9.30 lineage (A11.120, A11.119, A11.118 and A11.117) is visualized using the FGF8/17/18 reporter construct (blue nuclei).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Lateral view of a WT Ciona robusta late tailbud embryo probed for Dmbx (KH.C1.1212) expression. All embryos counterstained by fluorescent antibody stain for X-gal (red nuclei), denoting A9.30 lineage labeled by electroporation with Fgf8/17/18>lacZ.
A' is a higher magnification of A.
Original annotation:In situ hybridization of Dmbx in green, showing expression in only A12.239.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
No image shown in the article for this developmental stage.
Dmbx is expressed in A12.239 at the late tailbud stage.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Dorsal view of a Ciona robusta late tailbud embryo probed for Dmbx expression (green) and treated with DAPT.
Dmbx is expressed in A12.239 and A12.237.
Original comment: Treatment of embryos with Notch signaling inhibitor DAPT recapitulates FGF8/17/18>Su(H)-DBM phenotype. Inset is magnified view of boxed area. Filled and unfilled arrowheads indicate Dmbx ON and Dmbx OFF expression status, respectively.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Dorsal views of late tailbud stage embryo expressing Dmbx. The upper panel shows WISH signals, the middle DAPI signals and the lower the merged images.
Arrowheads indicate nuclei of the cells that express Dmbx. Open arrows indicate the constrictions in the row of nuclei of the lateral cells. Red dots indicate nuclei of the landmark cells.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | lateral VG ependymal cells - |
Two-color-fluorescence WISH was performed at the late tailbud stage (named stage Tr:Ta=1:3 in the paper). Dmbx expression is shown in red.
Ci-Dmbx is expressed in visceral ganglion.
Original annotation:Ci-Dmbx is expressed between the second and the third domains of Ci-En without any gap or overlapping.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Two-color fluorescence WISH was performed at the late tailbud stage. Dmbx expression is shown in red, SoxB1 in green.
Original annotation:
Ci-Dmbx is expressed in visceral ganglion . At this stage, the expression of Ci-SoxB1 was detected in four domains in the posterior trunk CNS. Ci-Dmbx is expressed between the second and third domains of Ci-SoxB1.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Two-color fluorescence WISH was performed at the late tailbud stage. Dmbx expression is shown in green, AChTP in red.
Original annotation:
Ci-Dmbx is expressed in visceral ganglion. The small anterior domain of Ci-vAChTP coincides with the Ci-Dmbx expression doamin.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Lateral view of the visceral ganglion of a WT Ciona robusta late tailbud embryo co-electroporated with Dmbx>unc76::GFP (green) and Fgf8/17/18>unc76::mCherry (red) reporter constructs.
Original annotation:A9.30 lineage is
labeled by electroporation of Fgf8/17/18>mCherry.
Colocalization of GFP and mCherry is indicated in
yellow and corresponds to Dmbx>GFP activity in A12.239.
A fusion of 3.5 kb of Dmbx upstream DNA with unc-76-tagged enhanced green fluorescent protein (GFP) recapitulated strong expression in A12.239, with slight expression in its sister cell, A12.240
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Lateral view of the visceral ganglion of a WT Ciona robusta late tailbud embryo co-electroporated with Dmbx>unc76::GFP (green) and Fgf8/17/18>unc76::mCherry (red) reporter constructs.
Original annotation:A9.30 lineage is
labeled by electroporation of Fgf8/17/18>mCherry.
Colocalization of GFP and mCherry is indicated in
yellow and corresponds to Dmbx>GFP activity in A12.239.
| Stained molecule | KH2012:KH.C5.5 (FGF17; FGF18; FGF8) |
| Stained region(s) | lateral VG ependymal cells - visceral ganglion - |
Lateral view of the motor ganglion of a WT Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>GFP (red nuclei) reporter constructs .
Dmbx reporter construct is active in A12.239.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei, cf diagram).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Lateral view of the motor ganglion of a WT Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>mCherry (red) reporter constructs and FGF8/17/18>Eph3ΔC overexpression construct.
Original comment: FGF8/17/18>Eph3ΔC results in abnormal Dmbx reporter expression, as a result of deregulation of Delta/Notch signaling and Pax3/7.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Lateral view of the motor ganglion of a Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>mCherry (red) reporter constructs and FGF8/17/18>Pax3/7 overexpression construct.
Original comment: Pax3/7 mis-expression activates ectopic Dmbx reporter expression in A9.30 progeny.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Dorsal view of the motor ganglion of a Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>mCherry (red) reporter constructs and FGF8/17/18>Pax3/7:WRPW overexpression construct.
Original comment: Overexpression of Pax3/7::WRPW completely abolishes Dmbx reporter.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | No expression - |
Dorsal view of the motor ganglion of a Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>mCherry (red) reporter constructs and En>Ngn:WRPW overexpression construct.
Original comment: ) En>Ngn::WRPW abolishes Dmbx reporter.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | No expression - |
Lateral view of the motor ganglion of a Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>mCherry (red) reporter constructs and En>dnFGFR overexpression construct.
Original comment: En>dnFGFR results in ‘twinning’ of Dmbx+ neurons (arrowheads).
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Lateral view of the motor ganglion of a Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>mCherry (red) reporter constructs, and En>dnFGFR and FGF8/17/18>Su(H)DBM overexpression constructs.
GFP is observed in A12.240, A12.239, A12.238 and A13.474.
Original comment: Combining both early Notch and late FGF perturbation [FGF8/17/18>Su(H)-DBM + En>dnFGFR] results in four Dmbx+ cells (two sets of ‘twins’).
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Lateral view of the motor ganglion of a Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>mCherry (red) reporter constructs and En>Dmbx overexpression construct.
GFP is expressed in A12.239 and A12.240.
Original comment: Electroporation of En>Dmbx also results in ‘twinning’ of A12.239.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Dorsal view of the motor ganglion of a Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>H2B:CFP (blue nuclei) reporter constructs and En>HA:SoxB1 (red) overexpression construct.
Original comment: SoxB1 overexpression abolishes Dmbx reporter expression.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (blue nuclei).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | No expression - |
Lateral view of the motor ganglion of a Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>H2B:CFP (blue nuclei) reporter constructs and En>HA:SoxB1 (red) and En>dnFGFR overexpression constructs.
Original comment: SoxB1 overexpression abolishes Dmbx reporter expression, overriding the ‘twinning’ phenotype of En>dnFGFR.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (blue nuclei).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | No expression - |
Dorsal view of the motor ganglion of a Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>H2B:CFP (blue nuclei) reporter constructs and En>HA:SoxB1 (red) and En>Dmbx overexpression constructs.
Original comment: SoxB1 overexpression abolishes Dmbx reporter expression, overriding the ‘twinning’ phenotype of En>Dmbx.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (blue nuclei).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | No expression - |
Lateral view of the motor ganglion of a Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>H2B:CFP (blue nuclei) reporter constructs and En>HA:SoxB1 (red) and En>Ngn overexpression constructs.
Original comment: Dmbx reporter expression is partially rescued by co-electroporation of En>Ngn.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (blue nuclei).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Lateral view of the motor ganglion of a Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>mCherry (red) reporter constructs and FGF8/17/18>Su(H)-DBM and FGF8/17/18>Eph3ΔC overexpression constructs.
Original comment: Inhibition of both Ephrin and Notch signaling results in all cells expressing Dmbx. As predicted by the model, FGF8/18/17>Eph3ΔC results in two A10.60-like cells, and FGF8/17/18>Su(H)-DBM results in four A11.120-like daughter cells from those two A10.60-like mother cells. Another round of cell division results in eight Dmbx+ A12.239-like cells on either side of the neural tube, perhaps owing to breakdown in later Notch and FGF signaling.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Lateral view of the visceral ganglion of a WT Ciona robusta late tailbud stage embryo probed for Dmbx expression (green) and electroporated with Fgf8/17/18>nlsLacZ (labels in red nuclei from A9.30 lineage) and COE>mCherry (no staining, control experiment).
Dmbx is expressed in A12.239, descending decussating neuron precursor.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | lateral VG ependymal cells - |
Dorsal view of the visceral ganglion of a Ciona robusta late tailbud stage embryo probed for Dmbx expression (green) and electroporated with Fgf8/17/18>nlsLacZ (labels in red nuclei from A9.30 lineage) and COE>Vsx overexpression construct. Dotted line represents the embryo midline, both hemispheres are visible but only the left side has been electroporated.
Original annotation: In Coe>Vsx condition, Dmbx expression is seen mainly in unelectroporated hemispheres, indicating that Vsx represses Dmbx. Left-right mosaic incorporation of plasmid thus provides us with an internal control. Arrow indicates A12.239.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | No expression - |
Dorsal view of the visceral ganglion of a Ciona robusta late tailbud stage embryo probed for Dmbx expression (green) and electroporated with Fgf8/17/18>nlsLacZ (labels in red nuclei from A9.30 lineage) and COE>Islet overexpression construct. Dotted line represents the embryo midline, both hemispheres are visible but only the left side has been electroporated.
Original annotation: In Coe>Islet, Dmbx expression is just as likely to be seen in
electroporated hemispheres as in unelectroporated hemispheres. This indicates relative lack of repression of Dmbx by Islet.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | lateral VG ependymal cells - |
No data shown in the article for this developmental stage.
Dmbx reporter construct is active in A12.239 at the late tailbud stage.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Dorsal view of the head of a Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>mCherry (red) reporter constructs and FGF8/17/18>Pax3/7 overexpression construct.
Dmbx reporter construct is active in A9.30, A9.29 and A9.32 progeny.
Original comment: Ectopic Dmbx+ neurons generated by Pax3/7 mis-expression project contralaterally. Nascent axon indicated by arrow.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei). Dashed line indicates midline.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Lateral view of the motor ganglion of a Ciona robusta late tailbud embryo electroporated with Dmbx>GFP (green) and FGF8/17/18>mCherry (red) reporter constructs and En>Delta2 overexpression construct.
Original comment: En>Delta2 also results in inversion of Dmbx expression pattern (n=51/100), presumably as a result of earlier inverted Pax3/7 expression.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei). Dashed line indicates midline.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Late tailbud embryo probed for Ci-Dmbx expression (in blue), Ci-En expression (in green) and Ci-SoxB1 expression (in red).
Original annotation:
According to the gene expression map (Ikuta and Saiga, 2007), expression of Ci-Dmbx was observed in A12.239 cell pair.
Aniseed annotation:
Corresponding fate of these cells : lateral visceral ganglion.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Late tailbud embryo probed for Ci-Dmbx expression (in blue), Ci-En expression (in green) and Ci-SoxB1 expression (in red) following the injection of Ci-Hox3-MO.
Original annotation:
Expression of the genes that share the expression domain with the Hox genes at tailbud or larval stage was unaffected in the tailbud embryos or larvae injected with MOs against Ci-Hox1, 2, 3, 4 and 5.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Whole mount in situ hybridization of Ciona embryo showing Ci-Dmbx expression at a swimming tadpole larva stage.
Original Annotation: expression is detected in the neural tube just behind the sensory vesicle; these cells are probably daughters of the cells expressing Ci-Dmbx in the neural tube. o, otolith and ocellar pigment spots.
Aniseed annotation:it seems that expression is localized in the visceral ganglion and in the sensory vesicle (near the otolith).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | posterior sensory vesicle - visceral ganglion - |
Dorsal and lateral views of swimming tadpole larva. Ci-Dmbx expression is observed in the visceral ganglion, just behind the sensory vesicle. These cells are probably daughters of the cells expressing Ci-Dmbx in neural tube at the tailbud stage. o, otolith and ocellar pigment spots (expression negative); vg visceral ganglion.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Larvae seen from the upper side.
Original annotation:
expression of Dmbx>CFP in the A12.239 lineage within the motor ganglion.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | visceral ganglion - |
Dorsal view of A12.239 pair from the visceral ganglion of a WT Ciona robusta swimming tadpole electroporated
with Dmbx>unc76::mCherry.
Original annotation:When embryos electroporated with such reporter constructs were allowed to develop until hatching, we were able to visualize individual terminally differentiated neurons. A12.239, as revealed by Dmbx>mCherry, shows a thin axon projecting down the tail. Furthermore, the A12.239 pair project contralaterally, each axon associating with the axon bundle on the opposite side of the embryo.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | motor neurones - |
Lateral view of the visceral ganglion of a WT Ciona robusta larva co-electroporated with Dmbx>unc76::CFP (blue), Vsx>unc76::mCherry (red), Nk6>unc76::YFP (green), and Islet>unc76::mCherry and Islet>unc76::CFP (purple) reporter constructs.
Dmbx enhancer drives CFP expression in A12.239 motor neuron.
Original annotation:Five motor neurons are simultaneously visualized and distinguishable from one another. Green channel was imaged on a different focal plane than blue or red, to visualize Nk6>YFP-labeled endplates. Yellow color only indicates overlap of cell bodies, not colocalization.
Diagram of the Ciona visceral ganglion ‘brainbow’ showing the neurons from the picture and their
unique morphological traits, such as contralateral projection of A12.239 pair, smaller cell body of A13.474, frondose endplates of A11.118, dendrites on A11.117, and elongated cell body and smaller endplates of A10.64 (motor neuron 2). Pale-green shading indicates left side of the larva. Pink fibers represent tail muscle.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | motor neurones - |
Lateral view of the visceral ganglion of a WT Ciona robusta larva co-electroporated with Dmbx>unc76::CFP (blue), Vsx>unc76::mCherry (red), Nk6>unc76::YFP (green), and Islet>unc76::mCherry and Islet>unc76::CFP (purple) reporter constructs.
Vsx enhancer drives mCherry expression in A13.474 and A11.117 motor neurons.
Original annotation:Five motor neurons are simultaneously visualized and distinguishable from one another. Green channel was imaged on a different focal plane than blue or red, to visualize Nk6>YFP-labeled endplates. Yellow color only indicates overlap of cell bodies, not colocalization.
(B) Diagram showing the neurons from the picture and their
unique morphological traits, such as contralateral projection of A12.239 pair, smaller cell body of A13.474, frondose endplates of A11.118, dendrites on A11.117, and elongated cell body and smaller endplates of A10.64 (motor neuron 2). Pale-green shading indicates left side of the larva. Pink fibers represent tail muscle.
| Stained molecule | KH2012:KH.C11.689 (ALX4; VSX1; VSX2) |
| Stained region(s) | motor neurones - |
Lateral view of the visceral ganglion of a WT Ciona robusta larva co-electroporated with Dmbx>unc76::CFP (blue), Vsx>unc76::mCherry (red), Nk6>unc76::YFP (green), and Islet>unc76::mCherry and Islet>unc76::CFP (purple) reporter constructs.
Nk6 enhancer drives YFP expression in A11.118 motor neuron (green).
Original annotation:Five motor neurons are simultaneously visualized and distinguishable from one another. Green channel was imaged on a different focal plane than blue or red, to visualize Nk6>YFP-labeled endplates. Yellow color only indicates overlap of cell bodies, not colocalization.
Diagram of the Ciona visceral ganglion ‘brainbow’ showing the neurons from the picture and their
unique morphological traits, such as contralateral projection of A12.239 pair, smaller cell body of A13.474, frondose endplates of A11.118, dendrites on A11.117, and elongated cell body and smaller endplates of A10.64 (motor neuron 2). Pale-green shading indicates left side of the larva. Pink fibers represent tail muscle.
| Stained molecule | KH2012:KH.C5.502 (NKX6-1; NKX6-2; NKX6-3) |
| Stained region(s) | motor neurones - |
Lateral view of the visceral ganglion of a WT Ciona robusta larva co-electroporated with Dmbx>unc76::CFP (blue), Vsx>unc76::mCherry (red), Nk6>unc76::YFP (green), and Islet>unc76::mCherry and Islet>unc76::CFP (purple) reporter constructs.
Islet enhancer drives mCherry and CFP expression in A10.64 motor neuron 2 (purple).
Original annotation:Five motor neurons are simultaneously visualized and distinguishable from one another. Green channel was imaged on a different focal plane than blue or red, to visualize Nk6>YFP-labeled endplates. Yellow color only indicates overlap of cell bodies, not colocalization.
Diagram of the Ciona visceral ganglion ‘brainbow’ showing the neurons from the picture and their
unique morphological traits, such as contralateral projection of A12.239 pair, smaller cell body of A13.474, frondose endplates of A11.118, dendrites on A11.117, and elongated cell body and smaller endplates of A10.64. Pale-green shading indicates left side of the larva. Pink fibers represent tail muscle.
| Stained molecule | KH2012:KH.L152.2 (ISL1; ISL2; LHX9) |
| Stained region(s) | motor neurones - |
Lateral view of the visceral ganglion of a WT Ciona robusta larva co-electroporated with Dmbx>unc76::CFP (blue), Vsx>unc76::mCherry (red), Nk6>unc76::YFP (green), and Islet>unc76::mCherry and Islet>unc76::CFP (purple) reporter constructs.
Islet enhancer drives mCherry and CFP expression in A10.64 motor neuron 2 (purple).
Original annotation:Five motor neurons are simultaneously visualized and distinguishable from one another. Green channel was imaged on a different focal plane than blue or red, to visualize Nk6>YFP-labeled endplates. Yellow color only indicates overlap of cell bodies, not colocalization.
Diagram of the Ciona visceral ganglion ‘brainbow’ showing the neurons from the picture and their
unique morphological traits, such as contralateral projection of A12.239 pair, smaller cell body of A13.474, frondose endplates of A11.118, dendrites on A11.117, and elongated cell body and smaller endplates of A10.64. Pale-green shading indicates left side of the larva. Pink fibers represent tail muscle.
| Stained molecule | KH2012:KH.L152.2 (ISL1; ISL2; LHX9) |
| Stained region(s) | motor neurones - |
Dorsal view of the visceral ganglion of a WT Ciona robusta larva co-electroporated with Nk6>unc76::GFP (green) and Dmbx>unc76::mCherry (red) reporter constructs.
Nk6 enhancer drives GFP expression in A11.118 motor neurons.
Original annotation:Co-electroporation of Nk6>GFP and Dmbx>mCherry further supported our conclusion that this late Nk6+ cell is A11.118 and that it is the only motoneuron to form the frondose endplates contacting the lateral surfaces of the anterior tail muscle cells.
(C') Magnified and different focal plane of boxed area to highlight frondose endplate labeled by the Nk6 reporter construct, but not by Dmbx reporter.
| Stained molecule | KH2012:KH.C5.502 (NKX6-1; NKX6-2; NKX6-3) |
| Stained region(s) | motor neurones - |
Dorsal view of the visceral ganglion of a WT Ciona robusta larva co-electroporated with Nk6>unc76::GFP (green) and Dmbx>unc76::mCherry (red) reporter constructs.
Dmbx enhancer drives mCherry expression in A12.239 motor neuron pair.
Original annotation: (C') Magnified and different focal plane of boxed area to highlight frondose endplate labeled by the Nk6 reporter construct, but not by Dmbx reporter.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | motor neurones - |
Dorsal view of the visceral ganglion of a WT Ciona robusta larva co-electroporated with Dmbx>unc76::GFP (green) and Fgf8/17/18>H2B::mCherry (red) reporter constructs.
Dmbx enhancer drives GFP expression in A12.239 motor neuron precursor.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | lateral VG ependymal cells - |
Dorsal view of the visceral ganglion of a WT Ciona robusta larva co-electroporated with Dmbx>unc76::GFP (green) and Fgf8/17/18>H2B::mCherry (red) reporter constructs.
Fgf8/17/18 enhancer drives mCherry expression in the nuclei of the A9.30 lineage cells.
| Stained molecule | KH2012:KH.C5.5 (FGF17; FGF18; FGF8) |
| Stained region(s) | lateral VG ependymal cells - visceral ganglion - |
Dorsal view of the visceral ganglion of a Ciona robusta larva co-electroporated with Dmbx>unc76::GFP (green) and Fgf8/17/18>H2B::mCherry (red) reporter constructs and Fgf8/17/18>Su(H)DBM overexpression construct.
Original annotation:Upon inhibition
of Notch signaling by co-electroporation with Fgf8/17/18>Su(H)DBM, Dmbx>GFP is seen to be expressed in two A9.30 descendants, instead of just A12.239.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | lateral VG ependymal cells - |
Dorsal view of the visceral ganglion of a Ciona robusta larva co-electroporated with Dmbx>unc76::GFP (green) and Fgf8/17/18>H2B::mCherry (red) reporter constructs and Fgf8/17/18>Su(H)DBM overexpression construct.
Nuclei from A9.30 lineage are labeled by electroporation with Fgf8/17/18>lacZ (red).
The asterisk denotes a mesenchyme cell expressing
Fgf8/17/18.
| Stained molecule | KH2012:KH.C5.5 (FGF17; FGF18; FGF8) |
| Stained region(s) | lateral VG ependymal cells - mesenchyme (B8.5 & B7.7 lines) - visceral ganglion - |
Lateral view of the head of a Ciona robusta larva co-electroporated with Dmbx>unc76::GFP (green) and Fgf8/17/18>H2B::mCherry (red) reporter constructs and COE>Vsx overexpression construct.
Nuclei from A9.30 lineage are labeled by electroporation with Fgf8/17/18>lacZ (red).
| Stained molecule | KH2012:KH.C5.5 (FGF17; FGF18; FGF8) |
| Stained region(s) | lateral VG ependymal cells - mesenchyme (B8.5 & B7.7 lines) - visceral ganglion - |
Lateral view of the head of a Ciona robusta larva co-electroporated with Dmbx>unc76::GFP (green) and Fgf8/17/18>H2B::mCherry (red) reporter constructs and COE>Vsx overexpression construct.
Original annotation: Vsx overexpression results in all A9.30 descendants expressing baseline levels of Dmbx>GFP (green), still visible but barely stronger than background.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | lateral VG ependymal cells - visceral ganglion - |
Lateral view of the motor ganglion of a WT Ciona robusta larva electroporated with Dmbx>GFP reporter construct.
Original comment: Visualization of A12.239 neuron pair by Dmbx>GFP. Note commissure resulting from A12.239 axons crossing the midline (arrow).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | motor neurones - |
Lateral view of the head of a Ciona robusta larva co-electroporated with Dmbx>GFP (green) and FGF8/17/18>H2B:mCherry (pink nuclei) reporter constructs and En>dnFGFR overexpression construct.
Dmbx regulatory element isactive in two motoneurons.
Original comment: The ectopic decussating neuron sometimes projects its axon anteriorly instead of towards the tail.
Nuclei of the A9.30 lineage are visualized with the FGF8/17/18 reporter construct.
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | motor neurones - |
Lateral view of the head of a WT Ciona robusta larva co-electroporated with wild-type (red) and mutated minimal (green) Dmbx reporter constructs.
Mutation of the predicted Pax3/7 site abolishes reporter activity (GFP expression seen in only 1/100 embryos).
| Stained molecule | KH2012:KH.C1.1212 (DMBX1; DRGX; PITX3) |
| Stained region(s) | No expression - |
Lateral view of the head of a WT Ciona robusta larva co-electroporated with wild-type (red) and mutated (green) minimal Dmbx reporter constructs.
WT Dmbx enhancer is active in A12.239 neuron pair.
| Stained molecule | KH2012:KH.C6.129 (NEUROG1; NEUROG2; NEUROG3) |
| Stained region(s) | motor neurones - |
