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| Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library |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| Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult |
|
6 clone(s) / 31,366 |
| Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo |
|
2 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| Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg |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| Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva |
|
9 clone(s) / 26,704 |
| Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo |
|
6 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| K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis |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| Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells |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| Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle |
|
1 clone(s) / 2,556 |
| Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo |
|
3 clone(s) / 16,939 |
| Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula |
|
2 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| Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad |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| Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex |
|
4 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| Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart |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| Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland |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| Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal |
|
1 clone(s) / 17,872 |
| Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal |
|
15 clone(s) / 107,314 |
| Nori Satoh unpublished cDNA library, juvenile whole animal Nori Satoh unpublished cDNA library, juvenile whole animal |
|
7 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) |
|
8 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) | |
28 results
Vegetal view with anterior to the top of a mid-gastrula stage embryo probed for Ci-aldh1a1/2/3a expression.
Original annotation: Expression was observed in the anterior muscle precursors.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | tail muscles - |
Vegetal view of a late gastrula stage embryo probed for Ci-Raldh2 expression. Embryos were treated with DMSO.
Original Annotation
Expression pattern in the DMSO-treated embryos was indistinguishable from that of untreated normal embryos. Ci-Raldh2 was first detected in four or five mesoderm cells on each side of the blastopore. These are muscle precursors and may also include a few mesenchyme precursors (mu, muscle).
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | tail muscles - |
Vegetal view of a late gastrula stage embryo treated with retinoic acid (RA). Control picture shows a late gastrula stage embryo treated with DMSO.
Original annotation:
Retinoic acid treatment did not severely affect Ci-Raldh2 expression pattern. Ra-induced reduction of Raldh2 expression was more evident in the mouse embryo (mu, muscle).
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | tail muscles - |
Dorsal view of an initial tailbud stage embryo probed for Ci-Raldh2 expression and treated with DMSO.
Original annotation:
Strong staining was observed only in three anterior most muscle cells and weak staining in the mesenchyme and other muscle cells, adjacent to the strongly stained cells (mu, muscle; mch, mesenchyme).
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | primary muscle lineage (anterior) - |
Dorsal view of an initial tailbud stage embryo treated with retinoic acid (RA). Control picture shows an initial tailbud stage embryo treated with DMSO.
Original annotation:
Retinoic acid treatment did not severely affect Ci-Raldh2 expression pattern. Ra-induced reduction of Raldh2 expression was more evident in the mouse embryo (mu, muscle; mch, mesenchyme).
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | primary muscle lineage (anterior) - |
Lateral and dorsal views of a tailbud wild type embryo probed for RaldH2 expression.
Original Annotation :
Expression was detected in the most anterior muscle cells.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | anterior ventral primary muscle lineage (B7.5 line) - antero central primary muscle lineage (B7.8 line) - |
Lateral view with anterior to the top of an early tailbud stage embryo probed for Ci-aldh1a1/2/3a expression.
Original annotation: Expression was observed in the anteriormost 3-5 muscle cell pairs.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | anterior ventral primary muscle lineage (B7.5 line) - antero central primary muscle lineage (B7.8 line) - |
Aniseed annotation:
Data and annotation provided by the author, not available in the article.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | anterior ventral primary muscle lineage (B7.5 line) - antero central primary muscle lineage (B7.8 line) - |
Lateral view of a mid tailbud stage embryo probed for Ci-Raldh2 and treated with DMSO.
Original annotation:
Strong staining was observed only in three anterior most muscle cells (mu).
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | anterior ventral primary muscle lineage (B7.5 line) - antero central primary muscle lineage (B7.8 line) - |
Lateral view of a mid tailbud stage embryo treated with retinoic acid (RA). Control picture shows a mid tailbud stage embryo treated with DMSO.
Original annotation:
Although expression was slightly downregulated, three anterior-most muscle cells did express C-Raldh2 mRNA. RA-induced reduction of Raldh2 expression was more evident in the mouse embryo.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | anterior ventral primary muscle lineage (B7.5 line) - antero central primary muscle lineage (B7.8 line) - |
Lateral view with anterior to the top of a mid-tailbud stage embryo probed for Ci-aldh1a1/2/3a expression.
Original annotation: Expression was observed in the anteriormost 3-5 muscle cell pairs.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | anterior ventral primary muscle lineage (B7.5 line) - antero central primary muscle lineage (B7.8 line) - |
Lateral view with anterior to the left of a mid-tailbud stage embryo probed for Ci-aldh1a1/2/3a expression.
Original annotation: Expression was observed in the anteriormost 3-5 muscle cell pairs.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | anterior ventral primary muscle lineage (B7.5 line) - antero central primary muscle lineage (B7.8 line) - |
Lateral view with anterior to the left of a mid-tailbud stage embryo probed for Ci-aldh1a1/2/3a expression, after retinoic acide treatment (1.5μM) at the late gastrula stage.
Original annotation: Expression was observed in the anteriormost 3-5 muscle cell pairs.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | anterior ventral primary muscle lineage (B7.5 line) - antero central primary muscle lineage (B7.8 line) - |
Lateral view with anterior to the left of a mid-tailbud stage embryo probed for Ci-aldh1a1/2/3a expression after DEAB treatment (150μM) at the late gastrula stage.
Original annotation: Expression was observed in the anteriormost 3-5 muscle cell pairs.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | anterior ventral primary muscle lineage (B7.5 line) - antero central primary muscle lineage (B7.8 line) - |
Lateral view with anterior to the left of a mid-tailbud stage embryo probed for Ci-aldh1a1/2/3a expression after bFGF treatment (10ng/ml) at the late gastrula stage.
Original annotation: Expression was observed in the anteriormost 3-5 muscle cell pairs.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | anterior ventral primary muscle lineage (B7.5 line) - antero central primary muscle lineage (B7.8 line) - |
Lateral view with anterior to the left of a mid-tailbud stage embryo probed for Ci-aldh1a1/2/3a expression after U0126 treatment (10μM) at the late gastrula stage.
Original annotation: Expression was lost in the anterior tail muscle cells.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | No expression - |
Lateral view of a late tailbud embryop probed for for Ci-Raldh2 expression. Expression is observed in the anterior tail muscles.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) | anterior ventral primary muscle lineage (B7.5 line) - |
Lateral view of the head of a WT Ciona robusta swimming larva probed for Raldh2 expression.
Raldh2 is expressed in the posterior trunk endoderm and anterior tail muscle cells.
Scale bar: 50 µm.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) |
Lateral view of the head of a Ciona robusta swimming larva probed for Raldh2 expression and electroporated with Titf>Hox1-TALEN. This overexpression construct is used to target the Hox1 locus in the endoderm.
Raldh2 is expressed in the posterior trunk endoderm and anterior tail muscle cells as in WT conditions.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) |
Lateral view of the head of a Ciona robusta swimming larva probed for Raldh2 expression and electroporated with Titf>Otx-TALEN. This overexpression construct is used to target the Otx locus in the endoderm.
Raldh2 is expressed in the posterior trunk endoderm and anterior tail muscle cells as in WT conditions.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) |
Lateral view of the head of a Ciona robusta swimming larva probed for Raldh2 expression and electroporated with Titf>RAR-TALEN. This overexpression construct is used to target the RAR (retinoic acid receptor) locus in the endoderm.
Raldh2 is expressed in the posterior trunk endoderm and anterior tail muscle cells as in WT conditions.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) |
WISH for Raldh2 in WT tail-absorbed Ciona robusta (30 hpf).
Raldh2 is expressed in the posterior endostyle (arrowhead). Anterior is to the left and dorsal is to the top.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) |
WISH for Raldh2 in tail-absorbed Ciona robusta (30 hpf) transfected with Titf>Hox1-TALEN. This overexpression construct is used to target the Hox1 locus in the endodermal tissue.
Raldh2 is no longer expressed in the posterior endostyle (dotted circle) when Hox1 is knocked out. Anterior is to the left and dorsal is to the top.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) |
WT Ciona robusta juvenile probed for Raldh2 expression.
Raldh2 is expressed in the posterior end of the endostyle (black arrowhead).
Scale bar: 50 µm.
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) |
Ciona robusta juvenile probed for Raldh2 expression and electroporated with Titf>Hox1-TALEN. This overexpression construct is used to target the Hox1 locus in the endodermal tissue.
Raldh2 expression in the posterior end of the endostyle is lost (white arrowhead).
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) |
Ciona robusta juvenile probed for Raldh2 expression and electroporated with Titf>Otx-TALEN. This overexpression construct is used to target the Otx locus in the endodermal tissue.
Raldh2 is expressed in the posterior end of the endostyle, as in WT conditions (black arrowhead), but also in its anterior end (red arrowhead).
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) |
Ciona robusta juvenile probed for Raldh2 expression and electroporated with Titf>Otx. This construct is used to overexpress Otx in the endodermal tissue.
Raldh2 expression in the posterior end of the endostyle, is lost (white arrowhead).
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) |
Ciona robusta juvenile probed for Raldh2 expression and electroporated with Titf>Hox1. This construct is used to overexpress Hox1 in the endodermal tissue.
Raldh2 is expressed in the posterior end of the endostyle, as in WT conditions (black arrowhead), but also in its anterior end (red arrowhead).
| Stained molecule | KH2012:KH.C4.697 (ALDH1A2; ALDH1A3; ALDH2) |
| Stained region(s) |
