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| Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library |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| Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult |
|
12 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| Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo |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| Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg |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| Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva |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| Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo |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| K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis |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| Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells |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| Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle |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| Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo |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| Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula |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| Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad |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| Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex |
|
2 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| Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart |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| Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland |
|
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| Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal |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 |
|
52 clone(s) / 107,314 |
| Nori Satoh unpublished cDNA library, juvenile whole animal Nori Satoh unpublished cDNA library, juvenile whole animal |
|
2 clone(s) / 24,372 |
| Nori Satoh unpublished cDNA library, mature adult whole animal Nori Satoh unpublished cDNA library, mature adult whole animal |
|
21 clone(s) / 17,126 |
| Ciona intestinalis whole animal stage3 juvenile Ciona intestinalis whole animal stage3 juvenile |
|
1 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 |
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) | |
12 results
Whole-mount in situ hybridization for Mhc3 in 3 days post fertilization Ciona robusta juveniles treated with dimethylsulfoxide (DMSO, control experiment).
Mhc3 is expressed in oral and atrial siphons and in the body wall muscles (BWM).
Numbers indicate the proportion of BWMs showing this phenotype.
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
Whole-mount in situ hybridization for Mhc3 in a 3 days post fertilization Ciona robusta juvenile treated with retinoic acid.
Mhc3 is expressed in oral and atrial siphons and in the body wall muscles (BWM). The BWM did not undergo elongation.
Numbers indicate the proportion of BWMs showing this phenotype.
Scale bar: 50 µm.
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
WT Ciona robusta 3 days post fertilization juveniles probed for Mhc3 expression.
Mhc3 is expressed in oral and atrial siphons and in the body wall muscles (BWM).
Numbers indicate the proportion of BWMs showing this phenotype.
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
Ciona robusta 3 days post fertilization juvenile probed for Mhc3 expression and treated with EtOH (control experiment).
Mhc3 is expressed in oral and atrial siphons and in the body wall muscles (BWM).
Numbers indicate the proportion of BWMs showing this phenotype.
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
WT Ciona robusta 3 days post fertilization juveniles probed for Mhc3 expression.
Mhc3 is expressed in oral and atrial siphons and in the body wall muscles (BWM).
Numbers indicate the proportion of BWMs showing this phenotype.
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
Ciona robusta 3 days post fertilization juvenile probed for Mhc3 expression and treated with EtOH (control experiment).
Mhc3 is expressed in oral and atrial siphons and in the body wall muscles (BWM).
Numbers indicate the proportion of BWMs showing this phenotype.
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
Ciona robusta 3 days post fertilization juveniles probed for Mhc3 expression and electroporated with Titf>Hox1-TALEN. This overexpression construct is used to target the Hox1 locus in the endodermal tissue.
Mhc3 is expressed in oral and atrial siphons and in the body wall muscles (BWM).
Original annotation: In Hox1 knockout juveniles, approximately 45% of observed BWMs displayed misdirected elongation (B) and 29% of them did not show elongation (C).
Numbers indicate the proportion of BWMs showing this phenotype.
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
Ciona robusta 3 days post fertilization juvenile probed for Mhc3 expression and treated with Citral (a retinoic acid synthesis inhibitor) from 45hpf.
Mhc3 is expressed in oral and atrial siphons, and in the body wall muscles (BWM).
Original comment: In the citral-treated condition, BWMs seemed to start the posterior elongation process but failed to complete it.
Numbers indicate the proportion of BWMs showing this phenotype.
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
Ciona robusta 3 days post fertilization juvenile probed for Mhc3 expression and electroporated with Titf>Raldh2-TALEN. This overexpression construct is used to target the Raldh2 locus in the endodermal tissue.
Mhc3 is expressed in oral and atrial siphons and in the body wall muscles (BWM).
Original comment: Knockout of Raldh2 in the endodermal tissue disrupted the elongation of BWMs.
Numbers indicate the proportion of BWMs showing this phenotype.
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
63 hpf Ciona robusta juvenile probed for MHC3 expression (green).
MHC3 mRNA signal colozalizes with B7.5 descendants in atrial siphon muscles (ASMs) and longitudinal muscles (LoMs), but not heart (Ht).
Differentiated B7.5 descendants are visualized using Mesp>LacZ staining (red).
C&D and C'&D' are different images of the
same juvenile taken at two different focal planes using a compound microscope.
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
In situ hybridization on wild-type Ciona robusta juveniles, showing MHC3 expression in atrial siphon muscles (arrow) and oral siphon (O.S.)
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
Ciona robusta juvenile probed for MHC3 expression and transfected with FoxF[TVC]>COE overexpression construct.
MHC3 is expressed in atrial siphon muscles (arrow) and oral siphon (O.S.), as in WT conditions.
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
Ciona robusta juvenile probed for MHC3 expression and transfected with FoxF[TVC]>COE::WRPW overexpression construct.
MHC3 is expressed in the oral siphon (O.S.), but overexpression of a COE dominant negative in the trunk ventral cells, abolishes MHC3 expression in the atrial siphon muscles. (arrow).
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
Conversion to Aniseed format of Ghost database entry from Ogasawara et al., Dev Genes Evol. 2002; 212:173-185. Original annotation: . Expression pattern: Body wall muscle
| Stained molecule | KH2012:KH.C3.774 (MYH2; MYH6; MYH7) |
| Stained region(s) |
