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| Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library |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| Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult |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| Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo |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| Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg |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| Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva |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| Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo |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| K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis |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| Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells |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| Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle |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| Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo |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| Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula |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| Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad |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| Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex |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| Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart |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| Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland |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| Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal |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 - |
