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Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library		1 clone(s) / 5,577
Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult		5 clone(s) / 31,366
Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo		0 clone(s) / 15,579
Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg		1 clone(s) / 31,100
Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva		7 clone(s) / 26,704
Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo		18 clone(s) / 26,680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K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis		0 clone(s) / 5,468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Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells		0 clone(s) / 29,579
Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle		0 clone(s) / 2,556
Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo		4 clone(s) / 16,939
Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula		3 clone(s) / 25,258
Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad		0 clone(s) / 16,936
Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex		0 clone(s) / 10,463
Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart		0 clone(s) / 13,243
Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland		1 clone(s) / 17,765
Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal		4 clone(s) / 17,872
Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal		2 clone(s) / 107,314
Nori Satoh unpublished cDNA library, juvenile whole animal Nori Satoh unpublished cDNA library, juvenile whole animal		5 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)		4 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

24 results

Click here to visualize with MorphoNet

Experiment data ( results)

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

Early neurula probed for Six1/2 (pink) and Eya (blue) expression, and electroporated with ZicL>GFP (yellow).
Original annotation : Dorsal view of an embryo at early neurula stage electroporated with ZicL>GFP and hybridized with Six1/2 and Eya mRNA probes. We found that the Ciona homologue of Six1, Six1/2, as well as its co-factor Eya, is initially expressed in a row of eight cells located immediately anterior to the neural plate (a10.77, a10.69, a10.101, a10.103), as marked by ZicL.

Stained molecule	KH2012:KH.C13.29 (MRPS7; RPS5)
Stained region(s)	a10.69 cell pair - a10.77 cell pair - a9.51 cell pair - a9.52 cell pair -

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

Dorsal view of an early Neurula wild type embryo probed for Ci-Eya alpha.

Original Annotation : Ci-Eya alpha expression was detected in mesenchyme and trunk lateral cells.

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)

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

Dorsal view of a mid neurula stage wild type embryo probed for Ci-Eya (alpha, beta, gamma) expression.

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	ectoderm primordia - siphon primordia -

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

Dorsal view of a neurula embryo probed for Ci-Eya gamma expression.

Original annotation : Faint expression of Ci-Eya gamma was detected at the neurula stage in future trunk lateral cells (arrow).

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)

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

Dorsal view of a late neurula stage wild type embryo probed for Ci-Eya beta expression.

Original annotation : Ci-Eya beta expression was detected in anterior ectoderm and faintly in prospective trunk lateral cells (arrow). "bc" means buccal cavity.

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	ectoderm primordia -

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

Lateral and dorsal views of an early tailbud stage embryo, showing expression of Ci-EyeA. Expression of Ci-EyeA was revealed by whole-mount in situ hydridization.

Stained molecule	KH2012:KH.C13.29 (MRPS7; RPS5)
Stained region(s)	anterior sensory vesicle - head endoderm -

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

Lateral view of a mid tailbud embryo probed for Ci-Eya alpha expression.

Original Annotation : Ci-Eya alpha expression was detected in mesenchyme (me) and trunk lateral cells (tlc).

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	trunk lateral cells (A7.6 line) -

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

Transverse sections through the head of mid tailbud embryo probed for Ci-Eya alpha expression. Dorsal is a the top and the neural tube is indicated (nt).

Original annotation : The picture shows that the expression of Ci-Eya alpha is restricted to the mesenchyme (me).

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)

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

Lateral view of a mid tailbud embryo probed for Ci-EYa gamma expression.

Original annotation : At this stage, faint expression of Ci-Eya gamma was detected in the mesoderm and trunk lateral cells (tlc).

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	mesoderm - trunk lateral cells (A7.6 line) -

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

Transverse sections through the head of mid tailbud embryo probed for Ci-Eya gamma expression. Dorsal is a the top and the neural tube is indicated (nt).

Original annotation : The picture shows that the expression of Ci-Eya gamma is faintly detected in the mesenchyme (me).

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)

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

Lateral view of a mid tailbud embryo probed for Ci-Eya beta expression.

Original annotation : Embryo stained for Ci-Eya beta, showing expression in the buccal cavity (bc) and in adjacent, more ventral ectoderm where the palps will develop (arrow). Dorsal staining in the trunk is ectodermal (e), other staining is mesenchymal (me).

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	ectoderm -

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

Transverse sections through the head of mid tailbud embryo probed for Ci-Eya beta expression. Dorsal is a the top and the neural tube (nt) is indicated.

Original annotation : The picture shows that the expression of Ci-Eya beta is found in both mesenchyme (me) and ectoderm (e).

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	ectoderm -

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

Mid tailbud wild type embryo probed for LacZ reporter expression for Ci-Eya enhancer.

Expression was detected strongly in the neurohypophysis primordium (anb), and less strongly in the mesenchyme (m), palps (p) and anterior epidermis (ae).

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	anterior dorsal midline head epidermis (a8.26 line) - central dorsal midline head epidermis (a7.14 line) - neurohypophysis primordium -

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

Mid tailbud wild type embryo probed for LacZ reporter expression for Ci-Eya enhancer.

Expression was detected strongly in the neurohypophysis primordium, palps, anterior epidermis and less strongly in the mesenchyme.

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	anterior dorsal midline head epidermis (a8.26 line) - central dorsal midline head epidermis (a7.14 line) - neurohypophysis primordium -

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

Dorsal and lateral view of a late tailbud embryo probed for Ci-Eya (all transcripts) expression.

Original annotation : Show staining is obtained with a probe common to all three transcrips (Ci-Eya alpha, Ci-Eya beta and Ci-Eya gamma). We can note staining in the buccal cavity and in ventral anterior ectoderm fated to form palps. On the pictures 'bc' means buccal cavity, 'me' means mesenchyme and 'e' for ectoderm, morevover the arrow shows the palps.

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)

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

Dorsal view of a late tailbud stage embryo, showing expression of Ci-EyeA. Expression of Ci-EyeA was revealed by whole-mount in situ hydridization.

Stained molecule	KH2012:KH.C13.29 (MRPS7; RPS5)
Stained region(s)	anterior sensory vesicle - head endoderm -

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

Lateral view of a late tailbud embryo probed for Ci-Eya alpha expression.

Original annotation : Expression of Ci-Eya alpha was confined to mesenchymal (me) and trunk lateral cells (tlc).

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	trunk lateral cells (A7.6 line) -

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

Lateral view of a late tailbud embryo probed for Ci-Eya beta expression.

Original annotation : Late tailbud stained for Ci-Eya beta, showing expression in the buccal cavity (bc) and in adjacent, more ventral ectoderm where the palps will develop (arrow). Dorsal staining in the trunk is ectodermal (e) and mesenchymal (me).

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	ectoderm -

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

Lateral view of a late tailbud embryo probed for Ci-Eya gamma expression.

Original annotation : At the late tailbud stage, expression of Ci-Eya gamma was activated in the buccal cavity (arrow).

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)

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

Conversion to Aniseed format of Ghost database entry from Kusakabe T et al., Dev Biol. 2002; 242:188-203. Original annotation: . Expression pattern: not detected

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	No expression -

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

Lateral view of an early larva embryo probed for Ci-Eya alpha expression.

Original annotation : Some background staining is present in tunic cells, but no other expression was detected.

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)

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

Early larva in lateral view probed for Ci-Eya beta expression.

Original annotation : Early larva stained for Ci-Eya beta, showing expression in the atrial promordium (ap) and adjacent mesenchyme.

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	atrial siphon primordia -

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

A view of a larva probed for Ci-Eya beta expression.

Original annotation : Show staining is obtained with a probe common to all three transcrips (Ci-Eya alpha, Ci-Eya beta and Ci-Eya gamma). Larva, showing faint expression in the atria (arrows) and posterior mesoderm (m). Darkly stained cells around the periphery are tunic cells. Staining of these cells is a background effect.

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	atrial siphon primordia - mesoderm -

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

A view of a Larva probed for Ci-Eya gamma expression.

Original annotation : At the larval stage no expression of Ci-Eya gamma was detected.

Stained molecule	KH2012:KH.C7.703 (EYA1; EYA2; EYA4)
Stained region(s)	No expression -