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| Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library |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| Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult |
|
4 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| Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo |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| Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg |
|
5 clone(s) / 31,100 |
| Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva |
|
4 clone(s) / 26,704 |
| Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo |
|
2 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| K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis |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| Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells |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| Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle |
|
4 clone(s) / 2,556 |
| Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo |
|
2 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| Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula |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| Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad |
|
1 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| Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex |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| Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart |
|
1 clone(s) / 13,243 |
| Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland |
|
2 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| Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal |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 |
|
6 clone(s) / 107,314 |
| Nori Satoh unpublished cDNA library, juvenile whole animal Nori Satoh unpublished cDNA library, juvenile whole animal |
|
4 clone(s) / 24,372 |
| Nori Satoh unpublished cDNA library, mature adult whole animal Nori Satoh unpublished cDNA library, mature adult whole animal |
|
2 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) |
|
3 clone(s) / 188,431 |
3 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) | ||
Ciona robusta adults were obtained from the National Bio-Resource Project for Ciona (NBRP, Japan). 50 unperturbed and Foxd-morphant embryos were collected at the 32-, 64-, and 112-cell stages. RNA was extracted using a Dynabeads mRNA DIRECT Purification Kit (Thermo Fischer Scientific) and libraries were made with an Ion Total RNA-Seq kit ver 2 (Thermo Fischer Scientific). The libraries were sequenced with an Ion PGM instrument (Thermo Fischer Scientific).
| Assay platform | Ion Torrent PGM | |
| Layout | Single-end | |
| Stranded | Yes | |
| Read length | 20-365 | |
| Normalized data types |
|
|
| Wild type | ||
| Territories | whole embryo - | |
| Biomaterial(s) | C. robusta formely Ciona int. type A, Stage 6a (early 32-cell) | |
| C. robusta formely Ciona int. type A, Stage 8 (64-cell) | ||
| C. robusta formely Ciona int. type A, Stage 10 (112-cell) | ||
| Mutant | ||
| Deregulated molecule(s) | KH2012:KH.C8.890 - | |
| Territories | whole embryo - | |
| Biomaterial(s) | C. robusta formely Ciona int. type A, Stage 6a (early 32-cell) | |
| C. robusta formely Ciona int. type A, Stage 8 (64-cell) | ||
| C. robusta formely Ciona int. type A, Stage 10 (112-cell) | ||
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) | |
33 results
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 :EphrinA-b.
Expression pattern : Unlocalized signal was detected.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | whole embryo - |
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 :EphrinA-b.
Expression pattern : No distinct zygotic signal was detected.
Comment : Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | whole embryo - |
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 :EphrinA-b.
Expression pattern : No distinct zygotic signal was detected.
Comment : Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | whole embryo - |
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 :EphrinA-b.
Expression pattern : No distinct zygotic signal was detected.
Comment : Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | whole embryo - |
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 :EphrinA-b.
Expression pattern : No distinct zygotic signal was detected.
Comment : Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | whole embryo - |
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 :EphrinA-b.
Expression pattern : No distinct zygotic signal was detected.
Comment : Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | whole embryo - |
Vegetal view of a late gastrula stage wild type embryo probed for EphrinA-b expression.
Original Annotation :
EphrinA-b was expressed in A9.29 cell pair.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | A9.29 cell pair - |
Vegetal view of a late gastrula stage embryo probed for EphrinA-b expression, following the injection of Snail-MO.
Original annotation:
Expression was lost in A9.29 cell pair (white arrow).
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | No expression - |
Vegetal view of a mid gastrula stage wild type embryo probed for Ci-ephrinAb expression.
Original Annotation : Ci-ephrinAb was expressed in neural plate more precisely in A.29 cell pair.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | A9.29 cell pair - |
Vegetal view of a mid gastrula stage embryo probed for Ci-ephrinAb expression following the injection of Delta2-MO.
Graph shows the percentage of embryo with ectopic, strong or weak Ci-ephrinAb expression ('Weak' means at least one cell with downregulated expression, 'strong' means at least one A-line precursor cell with strong expression, sometimes there is also 'ectopic' expression in column 4).
Original Annotation : Ci-ephrinAb expression was not affected by the inhibition of Delta2/Notch signaling due to Delta2-MO.
Occasionally, following disruption of Delta2/Notch signaling ectopic expression was seen for this gene.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | A9.29 cell pair - |
Vegetal view of a mid gastrula stage embryo probed for Ci-ephrinAb expression following the injection of DAPT.
Graph shows the percentage of embryo with ectopic, strong or weak Ci-ephrinAb expression ('Weak' means at least one cell with downregulated expression, 'strong' means at least one A-line precursor cell with strong expression and sometimes there is also 'ectopic' expression).
Original Annotation : Ci-ephrinAb expression was not affected by the inhibition of Delta2/Notch signaling due to DAPT. Occasionally, following disruption of Delta2/Notch signaling ectopic expression was seen for this gene.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | A9.29 cell pair - |
Vegetal view of a mid gastrula stage embryo probed for Ci-ephrinAb expression following the electroporation of the promoter FOG::Delta2.
Graph shows the percentage of embryo with ectopic, strong or weak Ci-ephrinAb expression ('Weak' means at least one cell with downregulated expression, 'strong' means at least one A-line precursor cell with strong expression).
Original Annotation : Ci-ephrinAb expression was not affected by the overexpression of Delta2/Notch signaling. But in some embryos Ci-ephrinAb appear slightly downregulated compared with control embryos.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | A9.29 cell pair - |
Vegetal view of a mid gastrula stage wild type embryo probed for Ci-ephrinAb expression.
Original Annotation : Ci-ephrinAb was expressed in neural plate more precisely in A.29 cell pair.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | A9.29 cell pair - |
Vegetal view of a mid gastrula stage embryo probed for Ci-ephrinAb expression following the treatment of a chemical agent : U0126.
Original Annotation : Ci-ephrinAb expression was lost following the inhibition of MEK/ERK due to U0126.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | No expression - |
Vegetative view of a mid gastrula. ephrin-Ab is expressed in A9.29 blastomere pair (row I of neural plate).
Aniseed annotation :
Very weak expression is also observed in neural plate row III .
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | A9.29 cell pair - row III neural plate - |
Vegetative view of a mid gastrula probed for Ephrin-Ab expression, following injection of Snail morpholino (Snail-MO (Imai's 25mer MO)).
Original annotation : Following injection of Snail morpholinos, ephrin-Ab (Efna.b) was down-regulated.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | No expression - |
Vegetative view of a mid gastrula probed for Ephrin-Ab expression, following injection of Snail morpholino (Snail-MO (Imai's 25mer MO)).
Original annotation : Following injection of Snail morpholinos, ephrin-Ab (Efna.b) was down-regulated.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | No expression - |
Vegetative view of a mid gastrula. ephrin-Ab is expressed in A9.29 blastomere pair (row I of neural plate).
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | A9.29 cell pair - |
Vegetative view of a mid gastrula probed for Ephrin-Ab expression, where Snail is overexpressed in medial lateral neural plate (electroporation of pETR>Snail). Signal is detected in A9.29 cell pair (WT expression pattern), but also in A9.13 and 9.15 cells (red arrowheads indicate ectopic expression).
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | A9.13 cell pair - A9.15 cell pair - A9.29 cell pair - |
Vegetative view of a mid gastrula probed for Ephrin-Ab expression and treated with SB431542 (Nodal inhibitor) until early gastrula stage. No signal was detected.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | No expression - |
Vegetative view of a mid gastrula probed for Ephrin-Ab expression, treated with SB431542 (Nodal inhibitor) until early gastrula stage and where Snail is overexpressed in medial lateral neural plate (electroporation of pETR>Snail). Signal is detected in A9.29 cells (WT expression pattern), but also in more medial cells of neural plate (rows I and II, red arrowheads indicate ectopic expression).
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | A9.13 cell pair - A9.15 cell pair - A9.16 cell pair - A9.29 cell pair - |
Vegetative view of a mid gastrula probed for Ephrin-Ab, where Nodal is overexpressed in animal territories (electroporation of pFOG>Nodal).
Original annotation :
Nodal overexpression was able to induce ectopic expression of Ephrin-Ab in their correct row of cells, row I.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | A9.13 cell pair - A9.15 cell pair - A9.29 cell pair - |
EphrinAb expression (red) in the A9.29 blastomeres of a late gastrula Ciona robusta embryo. Vegetal view.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | A9.29 cell pair - |
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 :EphrinA-b.
Expression pattern : nervous system.
Comment : Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | a line neural plate - A line neural plate - |
Vegetal pole view of a late gastrula stage wild type embryo probed for Ci-ephrinAb expression. Expression is detected in rowI/column3 (A9.29) of the neural plate. Numbers indicate any expression over the total number of embryos analysed.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | A9.29 cell pair - |
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 :EphrinA-b.
Expression pattern : nervous system.
Comment : Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | a line neural plate - A line neural plate - |
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 :EphrinA-b.
Expression pattern : nervous system, nerve cord.
Comment : Ventral nerve cord. A part of the brain. Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | anterior sensory vesicle - lateral VG ependymal precursors - ventral neck ependymal precursors - ventral TNC ependymal precursors (keel cells) - ventral VG ependymal precursors - |
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 :EphrinA-b.
Expression pattern : nervous system, nerve cord.
Comment : Ventral nerve cord. A part of the brain. Maternal signal were observed ubiquitously mainly in the early claeving stages, but also somewhat in the later stage.
Aniseed annotation : staining is also detected in palps on these pictures.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | neck - ventral TNC ependymal precursors (keel cells) - visceral ganglion - |
Dorsal view of a mid tailbud stage wild type embryo probed for EphrinA-b expression.
Red and yellow arrowheads indicate boundaries between the neck and the visceral ganglion, and between the visceral ganglion and the caudal nerve cord, respectively.
Original Annotation :
EphrinA-b expression in the visceral ganglion is localized in A12.240 cell pair.
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | visceral ganglion - |
Dorsal view of a mid tailbud stage embryo probed for EphrinA-b expression, following the injection of Pax3/7-MO.
Red and yellow arrowheads indicate boundaries between the neck and the visceral ganglion, and between the visceral ganglion and the caudal nerve cord, respectively.
Original Annotation :
EphrinA-b expression was lost in the visceral ganglion (white arrow).
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | No expression - |
Dorsal view of a mid tailbud stage embryo probed for EphrinA-b expression following the injection of EphrinA-b-MO.
Original Annotation :
Ectopic expression was observed in the tail nerve cord (black arrow).
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | tail nerve cord - visceral ganglion - |
Dorsal view of a mid tailbud stage embryo probed for EphrinA-b expression, following the injection of neurogenin-MO.
Original Annotation :
Expression was lost (white arrow).
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) | No expression - |
Conversion to Aniseed format of Ghost database entry from Ogasawara et al., Dev Genes Evol. 2002; 212:173-185. Original annotation: . Expression pattern: Endostyle Pharyngeal gill Stomach
| Stained molecule | KH2012:KH.C3.202 (EFNA1; EFNA5; EFNB2) |
| Stained region(s) |
