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Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library		1 clone(s) / 5,577
Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult		2 clone(s) / 31,366
Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo		0 clone(s) / 15,579
Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg		2 clone(s) / 31,100
Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva		7 clone(s) / 26,704
Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo		2 clone(s) / 26,680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K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis		1 clone(s) / 5,468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Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells		42 clone(s) / 29,579
Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle		0 clone(s) / 2,556
Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo		0 clone(s) / 16,939
Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula		2 clone(s) / 25,258
Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad		0 clone(s) / 16,936
Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex		4 clone(s) / 10,463
Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart		4 clone(s) / 13,243
Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland		0 clone(s) / 17,765
Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal		0 clone(s) / 17,872
Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal		4 clone(s) / 107,314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		3 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)		2 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

34 results

Click here to visualize with MorphoNet

Experiment data ( results)

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: the endoderm was very weakly stained.. Expression pattern: Notochord

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: the endoderm was very weakly stained.. Expression pattern: Notochord

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Lateral view of an early tailbud stage wild type embryo probed for Ci-talin expression. We can see expression in the notochord (arrowhead).

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Lateral view of an early tailbud stage embryo probed for Ci-talin expression following egg micro-injection of a Ci-Bra morpholino.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	No expression -

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

Lateral view of an early tailbud stage embryo probed for Ci-talin expression following egg micro-injection of a Ci-Bra morpholino.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Lateral view of an early tailbud stage wild type embryo probed for Ci-talin expression. We can see expression in the notochord cells.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Lateral view of an early tailbud stage wild type embryo probed for Ci-talin expression following egg micro-injection of a cieg003h01-MO.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	No expression -

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

Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: the endoderm was very weakly stained.. Expression pattern: Notochord

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Tailbud stage embryos probed for Ci-talin expression. No picture available in the paper.

Original Annotation :
Expression in notochord, and endoderm.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	endoderm - notochord -

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

Aniseed annotation:
Data and annotation provided by the author.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	head endoderm - notochord - trunk ventral cells (B7.5 line) -

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

Lateral view of a mid tailbud wild type stage embryo probed for Ci-talin expression.

Ci-talin was expressed in notochord.

Aniseed Annotation :
It seems that there is also expression of Ci-talin in the head endoderm.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	head endoderm - notochord -

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

Mid tailbud embryos probed for Ci-talin expression following the injection of Ci-Rga-MO.

Original Annotation : The expression of a notochord differentiation marker, Ci-talin, was lost or severely reduced in five (36%) or seven (50%) of 14 knock-down embryos.
First picture : Ci-Rga knock-down embryos with a weaker phenotype that develop into embryos covered by an epidermis layer.
Second picture : Ci-Rga knock-down embryos with severe phenotype that develop into cell aggregates.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	No expression -

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

Lateral view of a mid tailbud stage embryo probed with ci-talin expression.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Lateral view of a mid tailbud stage embryo probed with ci-talin expression. Embryos were injected with a MO against cieg007f18.

Original annotation: in the cieg007f18 knockdown embryos, whole-mount in situ hybridization showed that notochord was lost.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	No expression -

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

Lateral view of a mid tailbud stage embryo probed with Ci-talin expression. Embryos were injected with MO against cilv006h21.

Original annotation Embryos injected with MO against cilv006h21 were classified as " ball" phenotype: they developped into spherical-shaped cell masses, like balls. In these embryos, detection of the tissue specific markers indicated that almost the major tissues were lost or reduced.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	No expression -

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

Lateral view of a mid tailbud stage embryo probed with Ci-talin (notochord) expression. Expression of tissue-specific differenciation markers in morpholino oligonucleotide-injected embryos at the stage corresponding to the mid tailbud stage.

Original annotation: Embryos injected with MO against cieg009p15 as classified as " irregular" phenotype: embryos formed an irregular cellular mass. The a/p axis and trunk and tail could not be distinguished.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Original annotation: Embryos injected with MO against cieg039g16 is classified as " a/p axis" phenotype: embryos were extended along the anterior-posterior (a/p) axis, but did not form normal tadpoles, with head and tail being indistinguishable.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Original annotation: Embryos injected with MO against cicl017h21 is classified as " a/p axis" phenotype: embryos were extended along the anterior-posterior (a/p) axis, but did not form normal tadpoles, with head and tail being indistinguishable.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Original annotation: Embryos injected with MO against ciad033i21 is classified as " flat" phenotype: eggs develop into flattened larvae and they lost the expression of markers for endoderm, notochord and mesenchyme.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	No expression -

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

Lateral view of a mid tailbud stage embryo, showing expression of Ci-talin in notochord.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Lateral view of mid tailbud stage embryo, injected with Ci-FLJ10634 MO. Effects of functionnal suppression of Ci-FLJ10634 on differenciation of notochord (assessed by expression of Ci-talin).

Original annotation:
Embryos knocked down for Ci-FLJ10634 didn't show Ci-talin gene expression.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	No expression -

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

Lateral view of mid tailbud stage embryo, injected with Ci-Beta Catenin MO. Effects of functional suppression of Ci-Beta Catenin on differenciation of notochord (assessed by expression of Ci-talin).

Original annotation:
Embryos knocked down for Ci-Beta Catenin didn't show Ci-talin gene expression.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	No expression -

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

Lateral view of mid tailbud stage embryo, injected with Ci-C10orf11 MO. Effects of functional suppression of Ci-C10orf11 on differenciation of notochord (assessed by expression of Ci-talin).

Original annotation:
Embryos knocked down for Ci-C10orf11 didn't show Ci-talin gene expression.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	No expression -

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

Lateral view of mid tailbud stage embryo, injected with Ci-PGAP1 MO. Effects of functional suppression of Ci-PGAP1 on differenciation of notochord ( assessed by expression of Ci-talin).

Original annotation:
Embryos knocked down for Ci-PGAP1 didn't show Ci-talin gene expression.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	No expression -

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

Lateral view of mid tailbud stage embryo, injected with Ci-ZF278 MO. Effects of functional suppression of Ci-ZF278 on differenciation of notochord (assessed by expression of Ci-talin).

Original annotation:
Embryos knocked down for Ci-ZF278 didn't show Ci-talin gene expression.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	No expression -

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

Lateral view of mid tailbud stage embryo, injected with Ci-spatial MO. Effects of functional suppression of Ci-spatial on differenciation of notochord (assessed by expression of Ci-talin).

Original annotation:
Embryos knocked down for Ci-spatial didn't show Ci-talin gene expression.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	No expression -

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

Region upstream of Ci-talin from -1967bp to +107bp in front of a LacZ reporter. The construct was named p(-2.0k)talin/lacZ in the paper.

Original Annotation :
The p(-2.0k)talin/lacZ construct exhibited reporter gene expression in notochord cells and in mesenchyme cells.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Region upstream of Ci-talin from -2911bp to +107bp, in front of a LacZ reporter. The construct was named p(-3.0k)talin/lacZ in the paper.

Original Annotation :
The p(-3.0k)talin/lacZ construct exhibited reporter gene expression in notochord cells and in mesenchyme cells.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Region upstream of Ci-talin from -2448bp to +107bp i_n front of a LacZ reporter. The construct was named p(-2.5k)talin/lacZ in the paper.

Original Annotation :
The p(-2.5k)talin/lacZ construct exhibited reporter gene expression in notochord cells and in mesenchyme cells.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Region upstream of Ci-talin from -2163bp to +107bp in front of a LacZ reporter. The construct was named p(-2.3k)talin/lacZ in the paper.

Original Annotation :
The p(-2.3k)talin/lacZ construct exhibited reporter gene expression in notochord cells and in mesenchyme cells.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Region upstream of Ci-talin from -1411bp to +107bp in front of a LacZ reporter. The construct was named p(-1.5k)talin/lacZ in the paper.
The orange box indicates anterior A-lineage notochord specific regulatory region of the gene.

Original Annotation :
The p(-1.5k)talin/lacZ construct exhibited reporter gene expression in notochord cells and in mesenchyme cells.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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

Region upstream of Ci-talin from -908bp to +107bp, in front of a LacZ reporter. The construct was named p(-1.0k)talin/lacZ in the paper.

Original Annotation :
The p(-1.0k)talin/lacZ failed to drive reporter expression in notochord.
Ectopic expression was detected in the mesenchyme and muscle.

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	tail muscles -

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

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

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	notochord -

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 clear

Stained molecule	KH2012:KH.C3.14 (HIP1; TLN1; TLN2)
Stained region(s)	whole embryo -