Aniseed - Gene Card

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Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library		2 clone(s) / 5,577
Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult		1 clone(s) / 31,366
Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo		0 clone(s) / 15,579
Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg		0 clone(s) / 31,100
Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva		4 clone(s) / 26,704
Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo		0 clone(s) / 26,680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K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis		0 clone(s) / 5,468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Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells		0 clone(s) / 29,579
Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle		0 clone(s) / 2,556
Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo		1 clone(s) / 16,939
Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula		5 clone(s) / 25,258
Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad		0 clone(s) / 16,936
Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex		2 clone(s) / 10,463
Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart		0 clone(s) / 13,243
Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland		0 clone(s) / 17,765
Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal		1 clone(s) / 17,872
Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal		0 clone(s) / 107,314
Nori Satoh unpublished cDNA library, juvenile whole animal Nori Satoh unpublished cDNA library, juvenile whole animal		1 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)		7 clone(s) / 188,431

RNA-Seq transcriptome profiles (by Experiment)

3 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 2^RLE does not permit you to compare a gene across different experiments.

Download RLE Relative Log Expression data

RNA-Seq Experiment n°34135

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°34138

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	RPKM
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)

RNA-Seq Experiment n°34139

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

30 results

Click here to visualize with MorphoNet

Experiment data ( results)

C. robusta formely Ciona int. type A, Stage 1 (One cell)

Zygote embryo probed for Ci-CadherinII expression. No picture available in the article.

Original Annotation :
No signal.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)	No expression -

C. robusta formely Ciona int. type A, Stage 5a (early 16-cell)

Animal and vegetal views of a 16-cell stage embryo probed for Ci-CadherinII expression.

Original Annotation :
The Ci-CadherinII expression was detected in A5.1, A5.2 Comment: These signals were weak.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)	A5.1 cell pair - A5.2 cell pair -

C. robusta formely Ciona int. type A, Stage 6b (late 32-cell)

Animal and vegetal views of a 32-cell stage embryo probed for Ci-CadherinII expression.

Original Annotation :
The Ci-CadherinII expression was detected in A6.1, A6.2, A6.3, A6.4, B6.1, B6.2
Comments :
The gene expression in B6.2 was weaker than the expression in the other lineages.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)	A6.1 cell pair - A6.2 cell pair - A6.3 cell pair - A6.4 cell pair - B6.1 cell pair - B6.2 cell pair -

C. robusta formely Ciona int. type A, Stage 8 (64-cell)

Animal and vegetal views of a 64-cell stage embryo probed for Ci-CadherinII expression.

Original Annotation :
The Ci-CadherinII expression was detected in A-line cells and B-line cells, more precisely in A7.1, A7.2, A7.3, A7.4, A7.5, A7.6, A7.7, A7.8, B7.1, B7.2, B7.3, B7.4, B7.7, B7.8 cell pairs.
Comment :
Signals in B7.7 and B7.8 cell pairs were weak.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)	A line - B line -

C. robusta formely Ciona int. type A, Stage 8 (64-cell)

Vegetal view of 64cell-stage embryo probed for Ci-Cadherin2 expression. Nuclei are labeled with Hoechst (white) to allow easy identification of individual cells. Ci-Cadherin2 expression was detected in A7.1, A7.2, A7.3, A7.4, A7.5, A7.6, A7.7, A7.8, B7.1, B7.2, B7.3, B7.4, B7.7, B7.8 cell pairs.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)

C. robusta formely Ciona int. type A, Stage 8 (64-cell)

Animal view of 64cell-stage embryo probed for Ci-Cadherin2 expression. Nuclei are labeled with Hoechst (white) to allow easy identification of individual cells. Ci-Cadherin2 expression was not detected in a-line and b-line cells.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)

C. robusta formely Ciona int. type A, Stage 8 (64-cell)

Lateral view of 64cell-stage embryo probed for Ci-Cadherin2 expression. Nuclei are labeled with Hoechst (white) to allow easy identification of individual cells. Ci-Cadherin2 expression was detected in A7.1, A7.2, A7.3, A7.4, A7.5, A7.6, A7.7, A7.8, B7.1, B7.2, B7.3, B7.4, B7.7, B7.8 cell pairs.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)

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

Animal and vegetal views of an early gastrula stage embryo probed for Ci-CadherinII expression.

Original Annotation :
The Ci-CadherinII expression was detected in A-line cells and some cells of B-line, more precisely in A7.1, A7.2, A7.5, A7.6, A8.5, A8.6, A8.7, A8.8, A8.13, A8.14, A8.15, A8.16, B7.1, B7.2, B7.5, B7.7, B8.5, B8.6, B8.7, B8.8, B8.15, B8.16 cell pairs.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)	A line - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair - B7.7 cell pair - B8.15 cell pair - B8.16 cell pair - B8.5 cell pair - B8.6 cell pair - B8.7 cell pair - B8.8 cell pair -

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

Vegetal view of 112 cell-stage embryo probed for Ci-Cadherin2 expression. Nuclei are labeled with Hoechst (white) to allow easy identification of individual cells. Ci-Cadherin2 expression was detected in A7.1, A7.2, A7.5, A7.6, A8.5, A8.6, A8.7, A8.8, A8.13, A8.14, A8.15, A8.16, B7.1, B7.2, B7.5, B7.7, B8.5, B8.6, B8.7, B8.8, B8.15, B8.16 cell pairs.

Stained molecule

KH2012:KH.C12.14 (CDH18; CDH7; CDH8)

Stained region(s)

A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A8.11 cell pair - A8.12 cell pair - A8.13 cell pair - A8.14 cell pair - A8.15 cell pair - A8.16 cell pair - A8.5 cell pair - A8.6 cell pair - A8.7 cell pair - A8.8 cell pair - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair - B7.6 cell pair - B7.7 cell pair - B8.15 cell pair - B8.16 cell pair - B8.5 cell pair - B8.6 cell pair - B8.7 cell pair - B8.8 cell pair -

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

Animal view of 112-cell stage embryo probed for Ci-Cadherin2 expression. Nuclei are labeled with Hoechst (white) to allow easy identification of individual cells. Ci-Cadherin2 expression was not detected in a-line and b-line cells.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)

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

Lateral view of 112-cell stage embryo probed for Ci-Cadherin2 expression. Nuclei are labeled with Hoechst (white) to allow easy identification of individual cells. Ci-Cadherin2 expression was detected in A7.1, A7.2, A7.5, A7.6, A8.5, A8.6, A8.7, A8.8, A8.13, A8.14, A8.15, A8.16, B7.1, B7.2, B7.5, B7.7, B8.5, B8.6, B8.7, B8.8, B8.15, B8.16 cell pairs.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)

C. robusta formely Ciona int. type A, Stage 13 (late gastrula)

Animal and vegetal views of a late gastrula stage embryo probed for Ci-CadherinII expression.

Original Annotation :
The Ci-CadherinII expression was detected in endoderm, mesenchyme, muscle, nervous system (A9.13, A9.14, A9.15, A9.16, A9.29, A9.30, A9.32, a9.33, a9.34, a9.37, a9.38, b9.33, b9.37, b9.38), notochord, trunk ventral cells.
Comment :
Expression at the neural plate and in the trunk ventral cells was difficult to distinguish precisely because of the gene expression in other lineages.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)	A9.13 cell pair - A9.15 cell pair - A9.29 cell pair - A9.30 cell pair - A9.32 cell pair - a9.33 cell pair - a9.34 cell pair - a9.37 cell pair - a9.38 cell pair - b line neural plate - endoderm - notochord - tail muscles -

C. robusta formely Ciona int. type A, Stage 13 (late gastrula)

Dorsal view of late gastrula stage embryo probed for Ci-Cadherin2 expression. Nuclei are labeled with Hoechst (white) to allow easy identification of individual cells. The Ci-Cadherin2 expression was detected in endoderm, mesenchyme, muscle, nervous system (A9.13, A9.14, A9.15, A9.16, A9.29, A9.30, A9.32), notochord cells.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)

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

Vegetal view of a late gastrula stage embryo probed for Cadherin2 expression.

Original annotation :
Although low levels of Ci-cadherin2 is seen throughout the embryo, its expression level is enhanced in the A7.6/TLC lineage and other mesenchyme cells.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)

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

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)

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

Dorsal view of late gastrula stage embryo probed for Ci-Cadherin2 expression. Nuclei are labeled with Hoechst (white) to allow easy identification of individual cells. The Ci-Cadherin2 expression was detected in nervous system (A9.13, A9.14, A9.15, A9.16, A9.29, A9.30, A9.32, a9.33, a9.34, a9.37, a9.38, b9.33, b9.37, b9.38 ).

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)

C. robusta formely Ciona int. type A, Stage 15 (mid neurula)

No picture avaible. Cadherin-2 is expressed in the A7.6/TLC lineage at the neurula stage.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)

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

Dorsal view of a late neurula stage embryo probed for Ci-CadherinII expression.

Original Annotation :
The Ci-CadherinII expression was detected in the endoderm, mesenchyme and nervous system.
Comment :
Expression in endoderm was weak. Signals observed around the blastopore and those anterior to them were signals of nervous system.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)	endoderm - neural plate -

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

Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904.

Original annotation:
Expression pattern: endoderm, nerve cord, brain.

Aniseed annotation : A staining has been detected through the whole embryo and also in the nervous sytem, the visceral ganglion and in the head endoderm. A stronger staining has been detected in the tail nerve cord.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)	central nervous system - endoderm -

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

Dorsal view of an initial tailbud stage embryo probed for Cadherin2 expression.

Original annotation:
Although low level of Ci-cadherin2 was seen throughout the embryo, its expression level was enhanced in the A7.6/TLC lineage and other mesenchyme cells.

Stained molecule	KH2012:KH.C12.14 (CDH18; CDH7; CDH8)
Stained region(s)	endoderm - trunk lateral cells (A7.6 line) -