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EST count

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Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library 0 clone(s) / 5,577
Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult 54 clone(s) / 31,366
Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo 0 clone(s) / 15,579
Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg 0 clone(s) / 31,100
Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva 0 clone(s) / 26,704
Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo 0 clone(s) / 26,680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K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis 0 clone(s) / 5,468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Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells 3 clone(s) / 29,579
Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle 23 clone(s) / 2,556
Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo 0 clone(s) / 16,939
Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula 0 clone(s) / 25,258
Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad 0 clone(s) / 16,936
Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex 13 clone(s) / 10,463
Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart 47 clone(s) / 13,243
Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland 1 clone(s) / 17,765
Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal 0 clone(s) / 17,872
Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal 769 clone(s) / 107,314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 93 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) 1 clone(s) / 188,431

RNA-Seq transcriptome profiles (by Experiment)

2 results

OVERVIEW

   Expression profile summary from all experiments in WT and mutant conditions:
FPKM & RPKM

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.

Download FPKM & RPKM data

OVERVIEW

   Expression profile summary from all experiments in WT and mutant conditions:
Relative Log Expression RLE

Be careful, RLE and 2RLE does not permit you to compare a gene across different experiments.

Download RLE Relative Log Expression data

RNA-Seq Experiment n°34135

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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
  • FPKM
  • RLE
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)

RNA-Seq Experiment n°34139

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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
  • RPKM
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)

In Situ Experiment Data

34 results

Experiment data ( results)

C. robusta formely Ciona int. type A, Stage 10 (112-cell)

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Vegetal view of a 110-cell stage wild type embryo probed for Ci-actin expression. This picture shows expression in the muscle lineage cells.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) B8.15 cell pair - B8.16 cell pair - B8.7 cell pair - B8.8 cell pair -

C. robusta formely Ciona int. type A, Stage 10 (112-cell)

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Vegetal and lateral views of 110-cell stage embryos probed for Ci-actin expression. Embryos were injected with CiMDFb mRNA into eggs, which were then fertilized and examined for muscle-specific gene activity at 110-cell stage. In the injected embryos we can see an increase in the level of actin expression. These pictures shows expression of actin in the muscle (as in control) and in all the B-cell lineage that give rise to endoderm, mesenchyme and notochord.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) B line -

C. robusta formely Ciona int. type A, Stage 10 (112-cell)

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View of a 110-cell stage embryo showing expression of Ci-MA in muscle precursor cells.
Primary expression is in B8.7 and B8.8. Expression in B8.15/B8.16 is much weaker and barely visible.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) B8.7 cell pair - B8.8 cell pair -

C. robusta formely Ciona int. type A, Stage 10 (112-cell)

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Effects of knockdown of Ci-Tbx6b on the expression of muscle protein genes. Fertilized eggs were injected with Tbx6b and the expression of Ci-MA was examined at the 110-cell stage.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 10 (112-cell)

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Effects of knockdown of Ci-Tbx6c on the expression of muscle protein genes. Fertilized eggs were injected with Tbx6c and the expression of Ci-MA was examined at the 110-cell stage.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)

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Vegetal view of a mid gastrula stage wild type embryo probed for Ci-Actin expression. Cell division was blocked by cytochalasin B, gene expression profile corresponds to the stage observed.

original Annotation : Ci-Actin expression was detected in A9.32 and in B-muscle lineage.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) A9.32 cell pair - primary muscle lineage -

C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)

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Vegetal view of a mid gastrula stage embryo probed for Ci-Actin expression following the injection of a DAPT. Cell division was blocked by cytochalasin B, gene expression profile corresponds to the stage observed.
Graph shows the percentage of embryo with ectopic, strong or weak Ci-actin 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-Actin expression was affected by the inhibition of Delta2/Notch signaling, there is a loss of expression in A9.32 cell pair.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) primary muscle lineage -

C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)

Read more…

Vegetal view of a mid gastrula stage embryo probed for Ci-Actin expression, following the injection of a Delta2-MO. Cell division was blocked by cytochalasin B, gene expression profile corresponds to the stage observed.
Graph shows the percentage of embryo with ectopic, strong or weak Ci-actin 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-Actin expression was affected by the inhibition of Delta2/Notch signaling, there is a loss of expression in A9.32 cell pair.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) primary muscle lineage -

C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)

Read more…

Graph shows the percentage of embryo with ectopic, strong or weak Ci-actin expression following the injection of a dominant negative of Delta2, DnDel2. Cell division was blocked by cytochalasin B, gene expression profile corresponds to the stage observed. 'Weak' means at least one cell with downregulated expression, 'strong' means at least one A-line precursor cell with strong expression.

Original Annotation : Ci-Actin expression was affected by the inhibition of Delta2/Notch signaling, there is a loss of expression in A9.32 cell pair.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) primary muscle lineage -

C. robusta formely Ciona int. type A, Stage 14 (early neurula)

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Vegetal view of a early neurula stage embryo probed for Ci-OTX expression in which nodal signaling has been blocked from the 16-cell stage with SB431542. Control sibling embryo shows the wild type pattern of the gene and a control cleaving embryos for Ci-OTX expression. Cell division was blocked by cytochalasin B, gene expression profile corresponds to the stage observed.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) primary muscle lineage -

C. robusta formely Ciona int. type A, Stage 16 (late neurula)

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Vegetal view of a late neurula stage wild type probed for Ci-Actin expression. One of the embryos was normally cleaving the other was cleavage arrested with cytochalasin. expression is in primary and secondary muscle lineages.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) tail muscles -

C. robusta formely Ciona int. type A, Stage 16 (late neurula)

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Vegetal view of a early neurula stage embryo probed for Ci-Actin expression following egg micro-injection of a Nodal-MO. Nodal signalling is inhibited. Control sibling embryo shows the wild type pattern of the gene and a control cleaving embryos for Ci-OTX expression. Cell division was blocked by cytochalasin B.

expression is lost from the secondary muscle lineage and kept in the primary muscle lineage.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) primary muscle lineage -

C. robusta formely Ciona int. type A, Stage 16 (late neurula)

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Vegetal view of a early neurula stage embryo probed for Ci-muscle Actin expression following inhibition of nodal receptor type I by SB431542. Nodal signalling is inhibited. Control sibling embryo shows the wild type pattern of the gene and a control cleaving embryos for Ci-OTX expression. Cell division was blocked by cytochalasin B.

Expression is lost from the secondary muscle lineage and kept in the primary muscle lineage.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) primary muscle lineage -

C. robusta formely Ciona int. type A, Stage 17 (initial tailbud I)

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Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: . Expression pattern: Muscle(secodary lineage) Muscle(primary lineage)

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) primary muscle lineage (anterior) - secondary muscle lineage (posterior) -

C. robusta formely Ciona int. type A, Stage 19 (early tailbud I)

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Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: . Expression pattern: Muscle(secodary lineage) Muscle(primary lineage)

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) primary muscle lineage (anterior) - secondary muscle lineage (posterior) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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Lateral view of a mid-tailbud embryo probed with Ci-MA (Muscle Actin) expression.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) tail muscles -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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Injection of Ci-Tbx6b mRNA causes an expression of Ci-MA (Muscle Actin) in the whole embryo contrary to the control where Ci-MA is only expressed in tail-muscle cells.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) whole embryo -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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Injection of Ci-Tbx6b MO causes a light expression of Ci-MA (Muscle Actin) in the whole embryo, contrary to the control where Ci-MA is only expressed in tail-muscle cells. Note that a small pack of primary muscle lineage cells keeps a normal expression of Ci-MA.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) primary muscle lineage -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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Injection of Ci-Tbx6c mRNA causes an expression of Ci-MA (Muscle Actin) in the whole embryo contrary to the control where Ci-MA is only expressed in tail-muscle cells.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) whole embryo -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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Injection of Ci-Tbx6c MO strongly reduces and disturbs the expression of Ci-MA (Muscle Actin) in tail-muscle cells.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) tail muscles -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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View of a mid tailbud stage embryo, showing expression of Ci-MA in muscle cells. Embryos were cleavage arrested at the 100-cell stage by injection of cytochalasin B.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) tail muscles -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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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.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

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.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) tail muscles -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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Lateral view of a mid tailbud stage embryo, showing expression of Ci-MA in muscle cells.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) tail muscles -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Effects of simultaneous knockdown of Ci-Tbx6b/Ci-Tbx6c on the expression of muscle protein genes. The expression of Ci-MA was examined at the tailbud stage.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Effects of simultaneous knockdown of Ci-Tbx6b/Ci-Tbx6c/Ci-ZicL on the expression of muscle protein genes. The expression of Ci-MA was examined at the tailbud stage.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: . Expression pattern: Muscle(secodary lineage) Muscle(primary lineage)

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) primary muscle lineage - secondary muscle lineage -

C. robusta formely Ciona int. type A, Stage 23 (late tailbud I)

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Lateral view of a late stage wild type embryo probed for Ci-actin expression. This picture shows expression in the muscle cell lineage.

Aniseed annotation: it seems that there is also expression in the mesenchyme.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) tail muscles -

C. robusta formely Ciona int. type A, Stage 23 (late tailbud I)

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Lateral and dorsal views of a late tailbud stage embryo. These embryos were injected at egg stage with Ci-MRF mRNA and probed for Ci-Actin expression at late tailbud stage. The embryo did not develop normally and Ci-Actin is expressed in three-quarters of the cells.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) whole embryo -

C. robusta formely Ciona int. type A, Stage 23 (late tailbud I)

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Lateral pole view of a late tailbud stage wild type embryo probed for Ci-Actin expression.This picture shows expression in the tail muscle cell lineage.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) tail muscles -

C. robusta formely Ciona int. type A, Stage 23 (late tailbud I)

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Lateral pole view of late tailbud stage embryos probed for Ci-Actin expression in which Ci-MRF was blocked by Ci-MRF-MO1640. These pictures show an abnormal tail muscle formation.

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) secondary muscle lineage -

C. robusta formely Ciona int. type A, Stage 23 (late tailbud I)

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Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: . Expression pattern: Muscle(secodary lineage) Muscle(primary lineage)

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) primary muscle lineage - secondary muscle lineage -

C. robusta formely Ciona int. type A, Stage 26 (hatching larva)

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Conversion to Aniseed format of Ghost database entry from Kusakabe T et al., Dev Biol. 2002; 242:188-203. Original annotation: . Expression pattern: Epidermis

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s) epidermis -

C. robusta formely Ciona int. type A, Stage 48 (young adult)

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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 Stomach

Stained molecule KH2012:KH.C8.649 (ACTA1; ACTA2; ACTC1)
Stained region(s)