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Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library		2 clone(s) / 5,577
Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult		5 clone(s) / 31,366
Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo		4 clone(s) / 15,579
Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg		30 clone(s) / 31,100
Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva		8 clone(s) / 26,704
Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo		8 clone(s) / 26,680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K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis		0 clone(s) / 5,468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Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells		4 clone(s) / 29,579
Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle		1 clone(s) / 2,556
Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo		13 clone(s) / 16,939
Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula		7 clone(s) / 25,258
Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad		1 clone(s) / 16,936
Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex		1 clone(s) / 10,463
Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart		1 clone(s) / 13,243
Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland		0 clone(s) / 17,765
Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal		6 clone(s) / 17,872
Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal		7 clone(s) / 107,314
Nori Satoh unpublished cDNA library, juvenile whole animal Nori Satoh unpublished cDNA library, juvenile whole animal		4 clone(s) / 24,372
Nori Satoh unpublished cDNA library, mature adult whole animal Nori Satoh unpublished cDNA library, mature adult whole animal		5 clone(s) / 17,126
Ciona intestinalis whole animal stage3 juvenile Ciona intestinalis whole animal stage3 juvenile		2 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)		74 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

18 results

Click here to visualize with MorphoNet

Experiment data ( results)

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

Original annotation:
Pem localized signal was detected. The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression was detected.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	whole embryo -

C. robusta formely Ciona int. type A, Stage 3 (4-cell)

Original annotation:
No zygotic signal was detected.
The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

Aniseed annotation:
Pem localized signal was detected in B3 cell pair.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	whole embryo -

C. robusta formely Ciona int. type A, Stage 4 (8-cell)

Original annotation:
No zygotic signal was detected.
The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

Aniseed annotation:
Pem localized signal was detected in B4.1 cell pair.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	whole embryo -

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

Original annotation:
No zygotic signal was detected
The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

Aniseed annotation:
Pem localized signal was detected in B5.2 cell pair.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	whole embryo -

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

Original annotation:
No zygotic signal was detected.
The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

Aniseed annotation:
Pem localized signal was detected in B6.3 cell pair.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	whole embryo -

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

Original annotation:
No zygotic signal was detected.
The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

Aniseed annotation:
Pem localized signal was detected in B7.6 cell pair.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	B7.6 cell pair -

C. robusta formely Ciona int. type A, Stage 9 (76-cell)

Original annotation:
No zygotic signal was detected.
The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

Aniseed annotation:
Pem localized signal was detected in B7.6 cell pair.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	B7.6 cell pair -

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

Original annotation:
No zygotic signal was detected.
The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

Aniseed annotation:
Pem localized signal was detected in B7.6 cell pair. According to the picture, it seems that expression is also detected in B7.5 cell pair. Weak expression is detected through the whole embryo.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	B7.5 cell pair - B7.6 cell pair -

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

Animal view of a mid gastrula embryo for 00865 expression. 00865 encodes for a homologue of ciona savignyi pem3 gene in Ciona intestinalis genome.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	posterior endodermal strand (B7.6 line) -

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

Original annotation:
Staining is observed in the mesenchyme.
The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

Aniseed annotation:
Posterior blastomeres B7.6 cells produce two daughter cells names B8.11 and B8.12 cells (Shirae-Kurabayashi et al., in press). Ci-pem-3 is redistributed into B8.12 cells in addition to B8.11 cells. Weak staining is also detected through the whole embryo.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	B8.11 cell pair - B8.12 cell pair -

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

Original annotation:
Staining is observed in the mesenchyme.
The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	posterior endodermal strand (B8.11 line) - posterior endodermal strand (B8.12 line) -

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: Epidermis Endoderm Endodermal strand Neuron Mesenchyme

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	endodermal strand - epidermis - head endoderm - peripheral nervous system -

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

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	endodermal strand - epidermis - head endoderm - peripheral nervous system -

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

Original annotation:
Staining is observed in the mesenchyme and in the endodermal strand.
The expression in the posterior end/endodermal strand is maternal. B8.12-line cell expression were detected.

Aniseed annotation:
Posterior blastomeres B7.6 cells produce two daughter cells names B8.11 and B8.12 cells (Shirae-Kurabayashi et al., in press). Ci-pem-3 is redistributed into B8.12 cells in addition to B8.11 cells. Expression is also detected in the anterior endodermal strand. Weak expression is also detected in the epidermis.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	anterior endodermal strand (B7.2 line) - dorsal midline anterior tail epidermis - dorsal midline posterior tail epidermis - head epidermis - posterior endodermal strand (B8.11 line) - posterior endodermal strand (B8.12 line) - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis -

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:
Expression pattern: Epidermis Endoderm Endodermal strand Neuron Mesenchyme.

Aniseed annotation : a staining has been detected in the endoderm in the epidermis but also in the endodermal strand and in the part of the tail epidermis.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	endoderm - epidermis - peripheral nervous system -

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

Aniseed annotation:
Posterior blastomeres B7.6 cells produce two daughter cells names B8.11 and B8.12 cells (Shirae-Kurabayashi et al., in press). Ci-pem-3 is redistributed into B8.12 cells in addition to B8.11 cells. Expression is also detected in the anterior endodermal strand. Weak expression is also detected in the epidermis.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	anterior endodermal strand (B7.2 line) - head epidermis - posterior endodermal strand (B8.11 line) - posterior endodermal strand (B8.12 line) -

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: Epidermis Endoderm Endodermal strand Neuron Mesenchyme.

Aniseed annotation : a staining has been detected in the endoderm but also in the endodermal strand.

Stained molecule	KH2012:KH.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	endoderm - epidermis - peripheral nervous system -

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.S852.2 (MEX3B; MEX3C; MEX3D)
Stained region(s)	whole embryo -