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| Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library |
|
10 clone(s) / 5,577 |
| Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult |
|
3 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| Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo |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| Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg |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| Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva |
|
264 clone(s) / 26,704 |
| Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo |
|
117 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| K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis |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| Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells |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| Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle |
|
8 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| Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo |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| Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula |
|
18 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| Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad |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| Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex |
|
11 clone(s) / 10,463 |
| Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart |
|
57 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| Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland |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| Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal |
|
26 clone(s) / 17,872 |
| Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal |
|
157 clone(s) / 107,314 |
| Nori Satoh unpublished cDNA library, juvenile whole animal Nori Satoh unpublished cDNA library, juvenile whole animal |
|
59 clone(s) / 24,372 |
| Nori Satoh unpublished cDNA library, mature adult whole animal Nori Satoh unpublished cDNA library, mature adult whole animal |
|
20 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) |
|
4 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) |
|
19 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) | |
41 results
Vegetal view of a WT Ciona robusta late 32-cell stage embryo probed for TnT-b expression.
No expression is observed.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | No expression - |
Vegetal view of a WT Ciona robusta 64-cell stage embryo probed for TnT-b expression.
Expression is observed in A7.4, A7.8, B7.3, B7.4 and B7.8 blastomere pairs.
In schematic representation of gene expression, nerve cord precursors are shown in blue. Blastomeres with gene expression are marked by dots.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | A7.4 cell pair - A7.8 cell pair - B7.3 cell pair - B7.4 cell pair - B7.8 cell pair - |
View of a 110-cell stage embryo showing expression of Ci-TnT in muscle precursor cells.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | A8.15 cell pair - A8.16 cell pair - A8.7 cell pair - A8.8 cell pair - B8.15 cell pair - B8.7 cell pair - B8.8 cell pair - |
Effects of knockdown of Ci-Tbx6b on the expression of muscle protein genes. Fertilized eggs were injected with Tbx6b and the expression of Ci-TnT was examined at the 110-cell stage.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | No expression - |
Effects of knockdown of Ci-Tbx6c on the expression of muscle protein genes. Fertilized eggs were injected with Tbx6c and the expression of Ci-TnT was examined at the 110-cell stage. Expression in muscle precursors is affected.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | A8.15 cell pair - A8.7 cell pair - A8.8 cell pair - |
Vegetal view of a WT Ciona robusta 112-cell stage embryo probed for TnT-b expression.
Expression is observed in A8.7, A8.8, A8.15, A8.16, B7.7, B8.5, B8.7, B8.8, B8.15 and B8.16 blastomere pairs.
In schematic representation of gene expression, nerve cord precursors are shown in blue. Blastomeres with gene expression are marked by dots.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | A8.15 cell pair - A8.16 cell pair - A8.7 cell pair - A8.8 cell pair - B7.7 cell pair - B8.15 cell pair - B8.16 cell pair - B8.5 cell pair - B8.7 cell pair - B8.8 cell pair - |
Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: the entire body was stained very weakly.. Expression pattern: Muscle(secodary lineage) Muscle(primary lineage)
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | primary muscle lineage (anterior) - secondary muscle lineage (posterior) - |
Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904.
Original annotation:
the entire body was stained very weakly. Expression pattern: Muscle(secondary lineage) Muscle(primary lineage)
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | primary muscle lineage (anterior) - secondary muscle lineage (posterior) - |
Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: the entire body was stained very weakly.. Expression pattern: Muscle(secodary lineage) Muscle(primary lineage)
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | primary muscle lineage - secondary muscle lineage - |
Lateral view of a mid-tailbud stage embryo probed with Ci-TnT (Troponin T) expression.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | tail muscles - |
Injection of Ci-Tbx6b mRNA causes an expression of Ci-TnT (Troponin T) in a major part of the embryo contrary to the control where Ci-TnT is only expressed in tail-muscle cells.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | whole embryo - |
Injection of Ci-Tbx6c mRNA causes an expression of Ci-TnT (Troponin T) in the whole embryo contrary to the control where Ci-TnT is only expressed in tail-muscle cells.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | whole embryo - |
Injection of Ci-Tbx6b MO prevents the expression of Ci-TnT (Troponin T) contrary to the control where Ci-TnT is expressed in tail-muscle cells. Only two small sets of cells keep expression of Ci-TnT.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | primary muscle lineage - |
Injection of Ci-Tbx6c MO lightly reduces the expression of Ci-TnT (Troponin T) in tail-muscle cells.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | tail muscles - |
View of a mid tailbud stage embryo showing expression of Ci-TnT in muscle cells. Embryos were cleavage arrested in 110-cell stage by injection of cytochalasin B.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | tail muscles - |
Effects of knockdown of Ci-Tbx6b on the expression of muscle protein genes. Fertilized eggs were injected with Ci-Tbx6b MO. Expression was examined at the mid tailbud stage. Embryos were cleavage arrested at the 110-cell stage by injection of cytochalasin B.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | No expression - |
Effects of knockdown of Ci-Tbx6c on the expression of muscle protein genes. Fertilized eggs were injected with Ci-Tbx6c MO. Expression was examined at the mid tailbud stage. Embryos were cleavage arrested at the 110-cell stage by injection of cytochalasin B.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | tail muscles - |
Lateral view of a mid tailbud stage embryo, showing expression of Ci-TnT in muscle cells.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | tail muscles - |
Effects of simultaneous knockdown of Ci-Tbx6b/Ci-Tbx6c on the expression of muscle protein genes. Fertilized eggs were injected with MOs against Ci-Tbx6b and Ci-Tbx6c.
Later expression of these genes might be activated by mechanisms other than these two Tbx genes.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | primary muscle lineage - |
Effects of simultaneous knockdown of Ci-Tbx6b/Ci-Tbx6c/Ci-ZicL on the expression of muscle protein genes. The expression of Ci-TnT was examined at the tailbud stage.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | No expression - |
Aniseed annotation:
Data and annotation provided by the author, not available in the article.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | neck - posterior sensory vesicle - tail muscles - tail nerve cord - trunk ventral cells (B7.5 line) - visceral ganglion - |
Mid tailbud embryos were electroporated with a construct containing region -2191bp/74bp upstream Ci-TroponinT (TT construct #1610 in the paper).
No picture available in the article. This construct drives Ci-TroponinT expression in the muscle but the expression is less intense than in presence of Tbx6 and three CRE motfs.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | tail muscles - |
Mid tailbud embryos were electroporated with a construct containing region -542bp/74bp upstream Ci-TroponinT (TT construct #1163 in the paper).
No picture available in the article. This construct drives Ci-TroponinT expression in the muscle.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | tail muscles - |
Mid tailbud embryos were electroporated with a construct containing region -542bp/74bp upstream Ci-TroponinT (TT construct #1483 in the paper).
No picture available in the article. This construct is unable to drive Ci-TroponinT expression in the muscle probably due to the absence of the first CRE regulatory motif.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | No expression - |
Mid tailbud embryos were electroporated with a construct containing region -542bp/74bp upstream Ci-TroponinT (TT construct #1523 in the paper).
No picture available in the article. This construct is unable to drive Ci-TroponinT expression in the muscle probably due the mutation of the second CRE site.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | No expression - |
Mid tailbud embryos were electroporated with a construct containing region -542bp/74bp upstream Ci-TroponinT (TT construct #1485 in the paper).
No picture available in the article. This construct is unable to drive Ci-TroponinT expression in the muscle probably due to the mutation of the third CRE site.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | No expression - |
Mid tailbud embryos were electroporated with a construct containing region -512bp/74bp upstream Ci-TroponinT (TT construct #1050 in the paper).
No picture available in the article. This construct is unable to drive Ci-TroponinT expression in the muscle.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | No expression - |
Mid tailbud embryos were electroporated with a construct containing region -512bp/74bp upstream Ci-TroponinT (TT construct #1385 in the paper).
No picture available in the article. This construct is unable to drive Ci-TroponinT expression in the muscle probably due to the absence of Tbx6 site and the mutations in the second and the third CRE motifs.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | No expression - |
Mid tailbud embryos were electroporated with a construct containing region -497bp/74bp upstream Ci-TroponinT (TT construct #929 in the paper).
No picture available in the article. This construct is unable to drive Ci-TroponinT expression in the muscle.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | No expression - |
Mid tailbud embryos were electroporated with a construct containing region -484bp/74bp upstream Ci-TroponinT (TT construct #928 in the paper).
No picture available in the article. This construct is unable to drive Ci-TroponinT expression in the muscle.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | No expression - |
Mid tailbud embryos were electroporated with a construct containing region -457bp/74bp upstream Ci-TroponinT (TT construct #957 in the paper).
No picture available in the article. This construct is unable to drive Ci-TroponinT expression in the muscle.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | No expression - |
Mid tailbud embryos were electroporated with a construct containing region -497bp/74bp upstream Ci-TroponinT (TT construct #1382 in the paper).
No picture available in the article. This construct is unable to drive Ci-TroponinT expression in the muscle probably due to the absence of Tbx6 and first CRE motifs and the mutation of the third CRE motif.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | No expression - |
Mid tailbud embryos were electroporated with a construct containing region -2191bp/74bp upstream Ci-TroponinT (TT construct #1574 in the paper).
No picture available in the article. This construct drives Ci-TroponinT expression in the muscle.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | tail muscles - |
[Edit the insitu comment] Side view (anterior is to the left) of a late-tailbud embryo stained for Ci-TnT mRNA by in situ hybridization
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | neck - posterior sensory vesicle - tail muscles - trunk ventral cells (B7.5 line) - |
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) |
Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: the entire body was stained very weakly.. Expression pattern: Muscle(secodary lineage) Muscle(primary lineage)
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | primary muscle lineage - secondary muscle lineage - |
Conversion to aniseed format of DBTGR database entry from Kusakabe team.
Original annotation:
Muscle.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | tail muscles - |
Original annotation : Side view (anterior is to the left) of a late tailbud embryo electroporated with a lacZ transgene containing the -659 bp of the 5' flanking Ci-TnT promoter sequence to the -35 bp. Staining is restricted to the tail muscles, the trunk ventral cells and to the central nervous system as seen for the endogenous gene (see control).
Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates in the paper : -650bp/-50bp
Aniseed annotation : according to the picture, staining is also detected in the dorsal trunk ectoderm.
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | dorso lateral head epidermis - posterior sensory vesicle - tail muscles - trunk ventral cells (B7.5 line) - |
Conversion to Aniseed format of Ghost database entry from Kusakabe T et al., Dev Biol. 2002; 242:188-203. Original annotation: . Expression pattern: Muscle
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | tail muscles - |
Conversion to Aniseed format of Ghost database entry from Kusakabe T et al., Dev Biol. 2002; 242:188-203. Original annotation: . Expression pattern: Muscle
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) | tail muscles - |
Conversion to Aniseed format of Ghost database entry from Ogasawara et al., Dev Genes Evol. 2002; 212:173-185. Original annotation: ubiquitous. Expression pattern: Endostyle Pharyngeal gill Heart Intestine Body wall muscle Neural gland Epidermis Stomach Esophagus
| Stained molecule | KH2012:KH.C4.57 (TNNT1; TNNT2; TNNT3) |
| Stained region(s) |
