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Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library		0 clone(s) / 5,577
Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult		2 clone(s) / 31,366
Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo		0 clone(s) / 15,579
Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg		0 clone(s) / 31,100
Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva		0 clone(s) / 26,704
Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo		1 clone(s) / 26,680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K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis		0 clone(s) / 5,468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Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells		1 clone(s) / 29,579
Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle		0 clone(s) / 2,556
Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo		0 clone(s) / 16,939
Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula		0 clone(s) / 25,258
Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad		0 clone(s) / 16,936
Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex		0 clone(s) / 10,463
Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart		0 clone(s) / 13,243
Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland		0 clone(s) / 17,765
Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal		0 clone(s) / 17,872
Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal		0 clone(s) / 107,314
Nori Satoh unpublished cDNA library, juvenile whole animal Nori Satoh unpublished cDNA library, juvenile whole animal		3 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

45 results

Click here to visualize with MorphoNet

Experiment data ( results)

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

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Pax258-A.
Expression pattern : No signal was detected

Aniseed annotation :
Weak signal is detected through the embryo (maternal signal?).

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	whole embryo -

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

Conversion to Aniseed format of data from Yutaka Satous gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Pax258-A.
Expression pattern : No distinct zygotic signal was detected

Aniseed annotation :
Weak signal is detected through the embryo (maternal signal?).

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	whole embryo -

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

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Pax258-A.
Expression pattern : No distinct zygotic signal was detected

Aniseed annotation :
Weak signal is detected through the embryo (maternal signal?).

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	whole embryo -

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

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Pax258-A.
Expression pattern : No distinct zygotic signal was detected

Aniseed annotation :
No picture available at this stage.

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	whole embryo -

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

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Pax258-A.
Expression pattern : No distinct zygotic signal was detected

Aniseed annotation :
Weak signal is detected through the embryo.

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	whole embryo -

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

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Pax258-A.
Expression pattern : No distinct zygotic signal was detected

Aniseed annotation :
Weak signal is detected through the embryo.

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	whole embryo -

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

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Pax258-A.
Expression pattern : No distinct zygotic signal was detected

Aniseed annotation :
Weak signal is detected through the embryo.

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	whole embryo -

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

Vegetal view of a late gastrula stage embryo treated with U0126 from the 44-cell stage, and probed for Ci-Pax2/5/8-A expression.
Numbers indicate the total number of embryos analyzed.

Original Annotation :
There is no expression at this stage.

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	No expression -

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

Expression of CiPax2/5/8 at early neurula stage.

Original annotation: in early neurulae, CiPax2/5/8 was expressed in a bilateral pair of cells in the anrerior neural plate.

Aniseed annotation: according to the pictures, cells in which CiPax2/5/8 was expressed may be the precursors of the visceral ganglion cells.

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	A10.32 cell pair -

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

Conversion to Aniseed format of data from Yutaka Satous gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Pax258-A.
Expression pattern : nervous system.
Comment : ganglion

Aniseed annotation :
Cells that give ganglion at mid neurula stage are A10.28 cell pair, A10.30 cell pair, A10.31 cell pair, A10.32 cell pair, A10.58 cell pair, A10.59 cell pair, A10. 60, b9.38. It seems that there is no staining in A10.28 cell pair.

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	A10.30 cell pair - A10.31 cell pair - A10.32 cell pair - A10.58 cell pair - A10.59 cell pair - A10.60 cell pair - b9.38 cell pair -

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

Dorsal view of an initial tailbud stage embryo treated with U0126 from the early gastrula stage, and probed for Ci-Pax2/5/8-A expression.
Numbers indicate the total number of embryos analyzed.

Original Annotation :
Embryos treated with U0126 from the gastrula stage when FGF8/17/18 expression in A7.6 begins do not express Pax2/5/8-A.

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	No expression -

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

Dorsal view of an initial tailbud stage embryo treated with U0126 from the late gastrula stage, and probed for Ci-Pax2/5/8-A expression.
Numbers indicate the total number of embryos analyzed.

Original Annotation :
Embryos treated with U0126 from the late gastrula stage when FGF8/17/18 expression in A9.30 begins do not express Pax2/5/8-A.

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	No expression -

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

Conversion to Aniseed format of data from Yutaka Satous gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :Pax258-A.
Expression pattern : nervous system.
Comment : ganglion

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	neck - visceral ganglion -

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

Lateral view of an early tailbud stage embryo probed for CiPax2/5/8 expression

Aniseed annotation: According to the pictures, cells in which CiPax2/5/8 was expressed may be the precursors of the visceral ganglion cells.

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	visceral ganglion -

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

Lateral view of an early tailbud wild type embryo probed for Pax2/5/8 expression.
Red and yellow arrowheads indicate boundaries between the neck and the visceral ganglion, and between the visceral ganglion and the caudal nerve cord, respectively.

Original Annotation :
Pax2/5/8 was expressed in A11.61 and A11.62 cell pairs (neck).

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	neck -

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

Dorsal view of an early tailbud stage embryo probed for Pax2/5/8 expression, following the injection of FGF8/17/18 MO (FGF8/17/18-MO (Imai 2009)). Note that two FGF8/17/18 MOs were used in this article (in Aniseed FGF8/17/18-MO (Imai 2009) and FGF8/17/18-MO 2nd (Imai 2009)).
Red and yellow arrowheads indicate boundaries between the neck and the visceral ganglion, and between the visceral ganglion and the caudal nerve cord, respectively.

Original Annotation :
Expression in the neck was lost (white arrow).

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	No expression -

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

Dorsal view of an early tailbud stage embryo probed for Pax2/5/8 expression, following the injection of the second FGF8/17/18 MO (FGF8/17/18- 2nd MO (Imai 2009)). Note that two FGF8/17/18 MOs were used in this article (in Aniseed FGF8/17/18-MO (Imai 2009) and FGF8/17/18-2nd MO (Imai 2009)).
Red and yellow arrowheads indicate boundaries between the neck and the visceral ganglion, and between the visceral ganglion and the caudal nerve cord, respectively.

Original Annotation :
Expression in the neck was lost (white arrow).

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	No expression -

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

Dorsal view of an early tailbud stage wild type embryo probed for Ci-Pax2/5/8-A expression. The insert shows in red cells from the posterior sensory vesicle (PSV) and light-blue cells from the middle part of the visceral ganglion (VG). Broken white lines indicate the boundaries of the PSV/neck and the neck/VG.

Original Annotation :
Ci-Pax2/5/8-A expression was detected in A11.62 and A11.61 cell pairs (neck).

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	neck -

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

Dorsal view of an early tailbud stage embryo probed for Ci-Pax2/5/8-A expression, following the injection of FGF8/17/18 MO. The insert shows in red cells from the posterior sensory vesicle (PSV) and light-blue cells from the middle part of the visceral ganglion (VG). Broken white lines indicate the boundaries of the PSV/neck and the neck/VG.

Original Annotation :
Ci-Pax2/5/8-A expression was lost following the disruption of FGF8/17/18.

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	No expression -

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

Dorsal view of an early tailbud stage embryo treated with U0126 from the neurula stage, and probed for Ci-Pax2/5/8-A expression.
Numbers indicate the total number of embryos analyzed.

Original Annotation :
Embryos treated with U0126 from the neurula stage express Ci-Pax2/5/8-A.

Stained molecule	KH2012:KH.S1363.2 (KH.S1363.2)
Stained region(s)	neck -