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Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library		0 clone(s) / 5,577
Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult		0 clone(s) / 31,366
Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo		0 clone(s) / 15,579
Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg		0 clone(s) / 31,100
Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva		1 clone(s) / 26,704
Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo		1 clone(s) / 26,680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K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis		0 clone(s) / 5,468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Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells		0 clone(s) / 29,579
Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle		0 clone(s) / 2,556
Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo		0 clone(s) / 16,939
Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula		0 clone(s) / 25,258
Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad		0 clone(s) / 16,936
Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex		0 clone(s) / 10,463
Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart		0 clone(s) / 13,243
Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland		0 clone(s) / 17,765
Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal		0 clone(s) / 17,872
Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal		0 clone(s) / 107,314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

105 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 :Lhx3.
Expression pattern : No signal was detected

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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: Lhx3.
Expression pattern: No signal was detected.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16).

Original annotation :
Gene name: Lhx3.
Expression pattern: No zygotic signal was detected.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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 :Lhx3.
Expression pattern : No distinct zygotic signal was detected

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16).

Original annotation :
Gene name: Lhx3.
Expression pattern: No zygotic signal was detected.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - A6.3 cell pair - B6.1 cell pair -

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

Vegetal view of a Ciona robusta 32-cell stage embryo probed for Lhx3/4 expression and injected with Fgf9/16/20 MO.
Lhx3/4 is weakly expressed only in B6.1 blastomer pair. Lhx3/4 expression is lost in A-line cells.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	B6.1* -

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

Vegetal view of a Ciona robusta 32-cell stage embryo probed for Lhx3/4 expression and injected with Foxa.a MO.

Lhx3/4 is weakly expressed in B6.1 blastomer pair. Lhx3/4 expression is mostly lost in A-line cells.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	B6.1 cell pair - No expression -

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

Vegetal view of a Ciona robusta 32-cell stage embryo probed for Lhx3/4 expression and injected with Foxd MO.
Lhx3/4 is weakly expressed in B6.1 and A6.1 blastomer pairs.Lhx3/4 expression is lost in A6.3.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - B6.1 cell pair -

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

Vegetal view of a Ciona robusta 32-cell stage embryo probed for Lhx3/4 expression, injected with Foxd MO and treated with U0126 from the 16-cell stage.
Lhx3/4 expression is lost.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - A6.3 cell pair - B6.1 cell pair -

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

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.2 cell pair - A6.4 cell pair -

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

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)

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

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.2 cell pair - A6.4 cell pair - a6.5 cell pair - a6.6 cell pair - a6.7 cell pair - a6.8 cell pair - a line -

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

Experiment not described in the paper. Entry deduced from the article and from others ANISEED data.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - A6.3 cell pair - B6.1 cell pair -

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

Vegetal view of 32-cell stage embryo following the injection of the Tbx6b>beta-catenin construct and probed for Lhx3 expression.

Original Annotation :
Tbx6b > β-catenin transgene produces ectopic activation of Lhx3 in B-line muscle precursors.

Aniseed Annotation :
No control was available in the article but according to wild type expression profiles of Lhx3 already entered in ANISEED and according to the picture, it seems that expression was lost in A6.1, A6.3 and B6.1 cell pairs.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	B6.4 cell pair -

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

Animal view of 32-cell stage embryo following the injection of the BMP2>beta-catenin construct and probed for Lhx3 expression.

Original Annotation :
The bmp2b > beta-catenin transgene produces ectopic activation of Lhx3 in the animal hemisphere.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - a line - B6.1 cell pair - B6.3 cell pair - b line -

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

Vegetal view of a late 32-cell stage wild type embryo, showing expression of Ci-Lhx3.

According to the picture, Ci-Lhx3 was expressed in B6.1 cell pair, A6.2 cell pair, A6.3 cell and A6.1 cell pair.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - A6.2 cell pair - A6.3 cell pair - B6.1 cell pair -

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

Vegetal view of a late 32-cell stage embryos, showing expression of Ci-Lhx3 following the injection of Ci-Rga-MO.

Ci-Lhx3 was still expressed in B6.1 cell pair, A6.2 cell pair, A6.3 cell and A6.1 cell pair for 55% of embryos.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - A6.2 cell pair - A6.3 cell pair - B6.1 cell pair -

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 :Lhx3.
Expression pattern : A6.1, A6.3, B6.1

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - A6.3 cell pair - B6.1 cell pair -

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

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16).

Original annotation :
Gene name: Lhx3.
Expression pattern: A6.1 A6.3 B6.1.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - A6.3 cell pair - B6.1 cell pair -

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

Vegetal view of a late 32-cell stage embryo, showing expression of Ci-Lhx3.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - A6.3 cell pair - B6.1 cell pair -

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

Vegetal view of a late 32-cell stage embryo showing expression of Ci-Lhx3, following injection of Ci-Spatial/C4orf17 MO.

Original annotation:
The expression of Ci-Lhx3 became undetectable in embryos injected with morpholino against Ci-Spatial/C4orf17.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a late 32-cell stage embryo showing expression of Ci-Lhx3, following Ci-PGAP1 MO injection.

Original annotation:
The expression of Ci-Lhx3 became undetectable in embryos injected with morpholino against Ci-PGAP1.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a late 32-cell stage embryo showing expression of Ci-Lhx3, following injection of the Ci-ZF278 MO.

Original annotation:
The expression of Ci-Lhx3 became undetectable in embryos injected with morpholino against Ci-ZF278.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a late 32-cell stage embryo,showing no expression of Ci-Lhx3, following injection of Ci-C10orf11 MO.

Original annotation:
The expression of Ci-Lhx3 became undetectable in embryos injected with morpholino against Ci-C10orf11.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a late 32-cell stage embryo,showing no expression of Ci-Lhx3, following Ci-beta-catenin MO.

Original annotation:
The expression of Ci-Lhx3 became undetectable in embryos injected with morpholino against Ci-beta-catenin.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a late 32-cell stage embryo showing expression of Ci-Lhx3, following injection of Ci-FLJ10634 MO.

Original annotation:
The expression of Ci-Lhx3 became undetectable in embryos injected with morpholino against Ci-FLJ10634.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a late 32-cell stage embryo probed for Ci-Lhx3, in which eggs were injected with a mixture of DeltaN Ci-Beta Catenin mRNA and morpholino against Ci-beta-catenin.

Original annotation:
Injection of DeltaN Ci-Beta Catenin mRNA could restore the early expression of Ci-Lhx3 in embryos knocked down for Ci-beta-catenin.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A line - B line -

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

Vegetal view of a late 32-cell stage embryo probed for Ci-Lhx3, in which eggs were injected with a mixture of DeltaN Ci-Beta Catenin mRNA and morpholino against Ci-PGAP1.

Original annotation:
Injection of DeltaN Ci-Beta Catenin mRNA could restore the early expression of Ci-Lhx3 in embryos knocked down for Ci-PGAP1.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A line - B line -

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

Vegetal view of a late 32-cell stage embryo probed for Ci-Lhx3, in which eggs were injected with a mixture of DeltaN Ci-Beta Catenin mRNA and morpholino against Ci-ZF278.

Original annotation:
Injection of DeltaN Ci-Beta Catenin mRNA could restore the early expression of Ci-Lhx3 in embryos knocked down for Ci-ZF278.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A line - B line -

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

Vegetal view of a late 32-cell stage embryo probed for Ci-Lhx3, in which eggs were injected with a mixture of DeltaN Ci-Beta Catenin mRNA and morpholino against Ci-C10orf11.

Original annotation:
Injection of DeltaN Ci-Beta Catenin mRNA could restore the early expression of Ci-Lhx3 in embryos knocked down for Ci-C10orf11.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A line - B line -

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

Vegetal view of a late 32-cell stage embryo probed for Ci-Lhx3, in which eggs were injected with a mixture of DeltaN Ci-Beta Catenin mRNA and morpholino against Ci-spatial/C4orf17.

Original annotation:
Injection of DeltaN Ci-Beta Catenin mRNA could restore the early expression of Ci-Lhx3 in embryos knocked down for Ci-spatial/C4orf17.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A line - B line -

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

Vegetal view of a late 32-cell stage embryo probed for Ci-Lhx3, in which eggs were injected with a mixture of DeltaN Ci-Beta Catenin mRNA and morpholino against Ci-FLJ10634.

Original annotation:
Injection of DeltaN Ci-Beta Catenin mRNA could restore the early expression of Ci-Lhx3 in embryos knocked down for Ci-FLJ10634.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A line - B line -

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

Vegetal and lateral view of a late-32 cell stage embryo stained with Lhx3 expression. Red arrow point to the NN cells, blue arrow point to the E cell.
Original annotation: Expression observed in A6.1 and A6.3 cell pairs (E cells) with Lhx3. No expression in the animal cells.
Aniseed annotation: Expression is also observed in B6.1 cell pair.
(+HD photo)

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - A6.3 cell pair - B6.1 cell pair -

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

Vegetal and lateral view of a late-32 cell stage embryo stained with Lhx3 expression after BIO treatment at the late 16-cell stage. Red arrow point to the NN cells, blue arrow point to the E cell.
Original annotation: NN cell formation at the 32-cell stage is marked by expression of Lhx3 in A6.1, A6.2, A6.3, and A6.4. No expression in animal cells.
Aniseed annotation: Expression is also observed in B6.1 cell pair.
(+HD photo)

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - A6.2 cell pair - A6.3 cell pair - A6.4 cell pair - B6.1 cell pair -

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

Lateral view of a late-32 cell stage embryo stained with Lhx3 expression after BIO treatment at the late 8-cell stage.
Original annotation: Expression in all animal cells
Aniseed annotation: Expression observed in the entire embryo.
(+HD photo)

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	whole embryo -

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

Vegetal view of a late 32-cell stage embryo marked with Lhx3 after TCF∆C treatment at the 8-cell stage in A4.1 cell. The red arrow points the NN cells and the blue arrow the E cells. The green dashed line marks the region containing the cells from the A4.1 cell lineage.
Original annotation: Loss of expression in A6.1 (E cell).
Aniseed annotation: Normal expression in A6.3 and B6.1 cell pairs.
(+HD photo)

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.3 cell pair - B6.1 cell pair -

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

Vegetal view of a late 32-cell stage embryo marked with Lhx3 after TCF∆C treatment at the 16-cell stage in A5.1 cell. The red arrow points the NN cells and the blue arrow the E cells. The green dashed line marks the region containing the cells from the A5.1 cell lineage.
Original annotation: Loss of expression in A6.1 cell (E cell).
Aniseed annotation: Normal expression in the other A6.1 as well as the A6.3 and B6.1 cell pairs.
(+HD photo)

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.3 cell pair - B6.1 cell pair -

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

Vegetal view of a late-32 cell stage embryo stained with Lhx3 expression after Wnt5-MO treatment on the unfertelized egg. Red arrow point to the NN cells and the blue arrow the E cells.
Original annotation: Expression in E cells but not in NN cells.
Aniseed annotation: Expression is observed in A6.1, A6.3 and B6.1 cell pairs. (+ HD photos)

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - A6.3 cell pair - B6.1 cell pair -

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

Vegetal view of a late-32 cell stage embryo stained with Lhx3 expression after NotRNA treatment.
Original annotation: No expression either in NN or E cells. Aniseed annotation: Expression is not observed in the entire embryo.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a 32-cell stage wild type embryo probed for Ci-Lhx3a expression.

Original annotation:
No expression was detected at this stage.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a 32-cell stage wild type embryo probed for Ci-Lhx3b expression.

Original annotation:
Expression of Lhx3b were detected by WISH from the 32-cell stage onward in the endoderm producing cells, A6.1, A6.3 and B6.1 pairs.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A6.1 cell pair - A6.3 cell pair - B6.1 cell pair -

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

Vegetal view of a WT Ciona robusta 64-cell stage embryo probed for Lhx3/4 expression.
Lhx3/4 is expressed in A7.1, A7.2, A7.3, A7.5, A7.7, B7.1, B7.2 and B7.3 blastomer pairs.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.3 cell pair - A7.5 cell pair - A7.7 cell pair - B7.1 cell pair - B7.2 cell pair - B7.3 cell pair -

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

Vegetal view of a Ciona robusta 64-cell stage embryo probed for Lhx3/4 expression and treated with U0126 from the 16-cell stage.
Lhx3/4 expression is lost.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a Ciona robusta 64-cell stage embryo probed for Lhx3/4 expression and injected with morpholinos against Foxa.a.
Lhx3/4 expression is lost in the notochord lineage and strongly reduced in the other territories.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 - A7.2 cell pair -

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

Vegetal view of a Ciona robusta 64-cell stage embryo probed for Lhx3/4 expression and injected with morpholinos against Foxd.
Lhx3/4 expression is lost in the notochord lineage and strongly reduced in the other territories.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1* - A7.2* - B7.1* -

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

Vegetal view of a Ciona robusta 64-cell stage embryo probed for Lhx3/4 expression, injected with morpholinos against Foxd and treated with U0126 from the 16-cell stage.
Lhx3/4 expression is lost.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a WT Ciona robusta 64-cell stage embryo probed for Lhx3/4 expression.
Lhx3/4 is expressed in A7.1, A7.2, A7.3, A7.5, A7.7, B7.1, B7.2 and B7.3 blastomer pairs.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.3 cell pair - A7.5 cell pair - A7.7 cell pair - B7.1 cell pair - B7.2 cell pair - B7.3 cell pair -

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

Vegetal view of a Ciona robusta 64-cell stage embryo probed for Lhx3/4 expression and injected with morpholinos againts Fgf9/16/20.
Lhx3/4 expression is lost in the notochord lineage and strongly reduced in the other territories.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.5* - B7.1 cell pair - B7.2 cell pair -

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

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - B7.1 cell pair - B7.2 cell pair - B7.3 cell pair -

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

Vegetal view of a Ciona robusta 64-cell stage embryo probed for Lhx3/4 expression and injected with morpholinos against Foxd and Fgf9/16/20.
Lhx3/4 expression is lost.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a 64-cell stage embryo probed for Lhx3 expression.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.3 cell pair - A7.5 cell pair - A7.7 cell pair - B7.1 cell pair - B7.2 cell pair - B7.3 cell pair -

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

Vegetal view of a 64-cell stage embryo probed for Lhx3 expression following egg micro-injection of a Otx MO.

Orginal annotation : Expression was not affected.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.3 cell pair - A7.5 cell pair - A7.7 cell pair - B7.1 cell pair - B7.2 cell pair - B7.3 cell pair -

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

Vegetal view of a 64-cell stage embryo probed for Lhx3 expression following egg micro-injection of a FoxA-a MO.

Original annotation: most of the expression in vegetal cells were down-regulated but not all of the expression was lost.

Aniseed annotation: expression was lost in B7.1, B7.2 and B7.3

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.3 cell pair - A7.5 cell pair - A7.7 cell pair -

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

Vegetal view of a 64-cell stage embryo probed for Lhx3 expression following egg micro-injection of a ZicL MO.

Original annotation: Lhx3 was down-regulated in A-line notochord and the expression was not affected in endodermal cells.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - B7.1 cell pair - B7.2 cell pair - B7.3 cell pair -

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 :Lhx3.
Expression pattern : A7.1, A7.2, A7.3, A7.5, A7.7, B7.1, B7.2, B7.3

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.3 cell pair - A7.5 cell pair - A7.7 cell pair - B7.1 cell pair - B7.2 cell pair - B7.3 cell pair -

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

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16).

Original annotation :
Gene name: Lhx3.
Expression pattern: A7.1 A7.2 A7.3 A7.5 A7.7 B7.1 B7.2 B7.3

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.3 cell pair - A7.5 cell pair - A7.7 cell pair - B7.1 cell pair - B7.2 cell pair - B7.3 cell pair -

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

Vegetal view of a 64-cell stage wild type embryo probed for Ci-Lhx3a expression.

Original annotation:
No expression was detected at this stage.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a 64-cell stage wild type embryo probed for Ci-Lhx3b expression.

Original annotation:
The expression of Lhx3b continues in the endoderm lineage blastomeres (A7.1, A7.2, A7.5, B7.1, B7.2, B7.5) as well as the notochord and mesenchyme blastomeres (A7.3, A7.7, B7.3) at the 64-cell stage.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.3 cell pair - A7.5 cell pair - A7.7 cell pair - B7.1 cell pair - B7.2 cell pair - B7.3 cell pair - B7.5 cell pair -

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

Vegetal view of 110-cell stage wild type embryo probed for Lhx3 expression.

Aniseeed Annotation :
Lhx3 was expressed in endodermal cell precursors and weak expression is also observed in A-line notochord cells.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A8.5 cell pair - A8.6 cell pair - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair -

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

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16) Gene name: Lhx3. Original annotation: . Expression pattern: A7.1 A7.2 A7.5 B7.1 B7.2 B7.5

Aniseed annotation : Weak staining is also detected in A8.5, A8.6, A8.13, A8.14 cell pairs.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A8.13 cell pair - A8.14 cell pair - A8.5 cell pair - A8.6 cell pair - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair -

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 :Lhx3.
Expression pattern : A7.1, A7.2, A7.5, B7.1, B7.2, B7.5

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair -

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

Vegetal view of a 110-cell stage embryo probed for Lhx3 expression.

Original annotation: A7.1 A7.2 A7.5 B7.1 B7.2 B7.5

Aniseed annotation : weak staining may have been detected in A8.5, A8.6, A8.13, A8.14 cell pairs.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A8.13 cell pair - A8.14 cell pair - A8.5 cell pair - A8.6 cell pair - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair -

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

Vegetal view of a 112-cell stage wild type embryo probed for Ci-Lhx3a expression.

Original annotation:
No expression was detected at this stage.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a 112-cell stage wild type embryo probed for Ci-Lhx3b expression.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A8.13 cell pair - A8.14 cell pair - A8.5 cell pair - A8.6 cell pair - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair - B8.5 cell pair - B8.6 cell pair -

C. robusta formely Ciona int. type A, Stage 11 (early gastrula)

Vegetal view of a WT Ciona robusta early gastrula stage embryo probed for Lhx3 expression.
Lhx3, an endoderm marker, is expressed in B7.1, B7.2, B7.5, A7.1, A7.2 and A7.5 blastomere pairs.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair -

C. robusta formely Ciona int. type A, Stage 11 (early gastrula)

Vegetal view of a Ciona robusta early gastrula stage embryo probed for Lhx3 expression and injected with morpholino oligos against Eph-1.
Lhx3, an endoderm marker, is expressed in B7.1, B7.2, B7.5, A7.1, A7.2 and A7.5 blastomere pairs, as in WT conditions.
Original comment: Endoderm marker gene expression was not affected by Eph1 morpholino injection

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair -

C. robusta formely Ciona int. type A, Stage 11 (early gastrula)

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	A8.11 cell pair - A8.12 cell pair - A line - B7.2 cell pair -

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

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16).

Original annotation :
Gene name: Lhx3.
Expression pattern: nervous system.

Aniseed annotation : Very weak signal is detected in the neural plate but we can't localise precisely where. Signal is also detected in B7.5 cell pair.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	anterior ventral primary muscle lineage (B7.5 line) - neural plate -

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

Vegetal view of a gastrula stage wild type embryo probed for Ci-Lhx3a expression.

Original annotation:
No expression was detected at this stage.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Vegetal view of a gastrula stage wild type embryo probed for Ci-Lhx3b expression.

Aniseed Annotation :
At this stage, the staining was detected only B7.5 cell pair.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	anterior ventral primary muscle lineage (B7.5 line) -

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

Aniseed Comment : update of annotation of (Imai et al.,2004), based on (Imai et al.,2006).

Stained molecule

KH2012:KH.S215.4 (LHX3; LHX4; LHX5)

Stained region(s)

A10.27 cell pair - A10.28 cell pair - A10.31 cell pair - A10.32 cell pair - 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 - a9.35 cell pair - a9.36 cell pair - a9.37 cell pair - a9.38 cell pair - a9.39 cell pair - a9.40 cell pair - a9.49 cell pair - a9.50 cell pair - a9.51 cell pair - a9.52 cell pair - b9.33 cell pair - b9.37 cell pair - b9.38 cell pair -

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 :Lhx3.
Expression pattern : nervous system

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	neural plate -

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

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16)

Original annotation :
Gene name: Lhx3.
Expression pattern: nervous system.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	neural plate -

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

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	endoderm - notochord -

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

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 :Lhx3.
Expression pattern : nervous system

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	neural plate -

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

Dorsal view of a neurula stage wild type embryo probed for Ci-Lhx3a expression.
Insets are specimens detected for the transcripts of Ci-Lhx3a by WISH using the probe covering the 4th, 5th and 6th exons of Ci-Lhx3.

Original Annotation :
Zygotic expression of Lhx3a becomes detectable by WISH from the neurula stage onward in the cells at the neural fold.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	neural plate -

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

Dorsal view of a neurula stage wild type embryo probed for Ci-Lhx3b expression.

Original annotation:
According to the paper, no expression was detected at this stage.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16)

Original annotation :
Gene name: Lhx3.
Expression pattern: nervous system.

Aniseed annotation :
According to the other developmental stages and to the picture, it seems that staining is localised in the precursors of the visceral ganglion and in the precursors of the anterior sensory vesicle.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	a10.100 cell pair - A10.30 cell pair - A10.31 cell pair - A10.58 cell pair - A10.59 cell pair - A10.60 cell pair - a10.68 cell pair - a10.76 cell pair - a10.98 cell pair - a10.99 cell pair - b10.75 cell pair - b10.76 cell pair -

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

Lateral view of an early tailbud stage embryo, showing expression of Ci-Lhx3. Expression of Ci-Lhx3 was revealed by whole-mount in situ hydridization.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	anterior sensory vesicle - visceral ganglion -

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

Dorsal view of an early tailbud stage wild type embryo probed for Lhx3.
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 :
Lhx3 was expressed in the visceral ganglion more precisely in A11.118, A11.117 and A10.57 cell pairs.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	visceral ganglion -

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

Dorsal views of early tailbud stage embryo expressing Lhx3. The upper panel shows WISH signals, the middle DAPI signals and the lower the merged images.
Arrowheads indicate nuclei of the cells that express Lhx3. Open arrows indicate the constrictions in the row of nuclei of the lateral cells. Red dots indicate nuclei of the landmark cells.

Original annotation:
Ci-vAChTP and Ci-Lhx3 are co-expressed in the three landmark cells on each side.
NB: All genes described in figure 4 are expressed exclusively in the lateral cell rows.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	lateral TNC ependymal precursors - lateral VG ependymal precursors -

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

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16) Gene name: Lhx3.

Original annotation:
Expression pattern: nervous system.
Comment : ganglion and the anterior region of the brain.

Aniseed annotation : a staining has been detected in part of the central nervous system but also in the anterior sensory vesicle and the visceral ganglion.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	anterior sensory vesicle - visceral ganglion -

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

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 :Lhx3.
Expression pattern : nervous system

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	nervous system -

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

Two-color-fluorescence WISH was performed at the early tailbud stage. Lhx3 expression is shown in green, Hox1 in red.

Original annotation:
Ci-Lhx3 is expressed in visceral ganglion and in part of the tail nerve cord.
The anterior expression domain of Ci-Lhx3 is located in the gap between the two expression domains of Ci-Hox1, and the posterior domain of Ci-Lhx3 is located postero-lateraly in relation to the second domain of Ci-Hox1. Ci-Lhx3 showed the same expression pattern as Ci-vAChTP.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	tail nerve cord - visceral ganglion -

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

Lateral view of the motor ganglion of a WT Ciona robusta early tailbud embryo probed for Lhx3 expression (red) and electroporated with Fgf8/17/18>LacZ reporter construct (green nuclei).
Lhx3 is expressed in A11.118 and A11.117 motor neuron precursors (arrowheads).
Original comment: Nuclei of the A9.30 lineage are visualized by immunofluorescence detection of nuclear β-galactosidase reporter (green) driven by the FGF8/17/18 driver (cf diagram).

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	visceral ganglion -

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-Lhx3a expression.
Insets are specimens detected for the transcripts of Ci-Lhx3a by WISH using the probe covering the 4th, 5th and 6th exons of Ci-Lhx3.

Original Annotation :
Zygotic expression of Lhx3a becomes detectable in a part of brain and the visceral ganglion cells at the tailbud stages.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	anterior sensory vesicle - visceral ganglion -

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-Lhx3b expression.

Original annotation:
No expression was detected at this stage.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Mid tailbud stage wild type embryo probed for Lhx3. No picture available in the article.

Original Annotation :
Lhx3 was expressed in the visceral ganglion more precisely in A11.118 and A11.117 cell pairs.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	visceral ganglion -

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

Dorsal views of mid tailbud stage embryo expressing Lhx3. The upper panel shows WISH signals, the middle DAPI signals and the lower the merged images.

Arrowheads indicate nuclei of the cells that express Lhx3. Open arrows indicate the constrictions in the row of nuclei of the lateral cells. Red dots indicate nuclei of the landmark cells.

Original annotation:
Expression of Ci-Lhx3 is detected in five cells on each side, and the posterior three cells correspond to the M2, M3 and M4 cells.
NB: All genes described in figure 4 are expressed exclusively in the lateral cell rows.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	lateral TNC ependymal precursors - lateral VG ependymal precursors -

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

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16) Gene name: Lhx3.

Original annotation:
Expression pattern: nervous system.
Comment : ganglion and the anterior region of the brain.

Aniseed annotation: a staining has been detected in the part of the anterior sensory vesicle and in the visceral ganglion.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	anterior sensory vesicle - visceral ganglion -

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

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 :Lhx3.
Expression pattern : nervous system

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	nervous system -

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

Two-color-fluorescence WISH was performed at the mid tailbud stage. Lhx3 expression is shown in green, Hox1 in red.

Original annotation:
Ci-Lhx3 is expressed in the visceral ganglion and in part of the tail nerve cord. The anterior domain of Ci-Lhx3 extends anteriorly up to the posterior part of the first Ci-Hox1 domain.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	tail nerve cord - visceral ganglion -

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

Two-color-fluorescence WISH was performed at the mid tailbud stage. Lhx3 expression is shown in red, Fgf8/17/18 in green.
Ci-Lhx3 is expressed in the visceral ganglion and in part of the tail nerve cord.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	tail nerve cord - visceral ganglion -

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

Two-color-fluorescence WISH was performed at the mid tailbud stage. Lhx3 expression is shown in green, SoxB1 in red.

Original annotation:
Ci-Lhx3 is expressed in the visceral ganglion and in part of the tail nerve cord. The overlapping of Ci-Lhx3 and Ci-Hox1 expression is located just posterior to the second domain of Ci-SoxB1.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	tail nerve cord - visceral ganglion -

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

Lateral view of a mid tailbud stage wild type embryo probed for Ci-Lhx3a expression.
Insets are specimens detected for the transcripts of Ci-Lhx3a by WISH using the probe covering the 4th, 5th and 6th exons of Ci-Lhx3.
Last picture : the anterior dorsal view of the WISH specimen shown in the inset of the panel indicating the mid tailbud stage for Ci-Lhx3. A and P stand for the anterior and posterior of the trunk, respectively.

Original Annotation :
Zygotic expression of Lhx3a becomes detectable in a part of brain and the visceral ganglion cells at the tailbud stages. Lhx3a is expressed at the mid tailbud stage in the anterior-dorsal trunk. The cells expressing Ci-Lhx3a seemed to correspond to the precursors of the larval rostral trunk epidermal neurons (RTEN).

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	anterior sensory vesicle - rostral trunk epidermal neurone precursors (RTEN) (a8.26 line) - visceral ganglion -

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

Lateral view of a mid tailbud stage wild type embryo probed for Ci-Lhx3b expression.

Original annotation:
No expression was detected at this stage.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	No expression -

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

Dorsal views of late tailbud stage embryo expressing Lhx3. The upper panel shows WISH signals, the middle DAPI signals and the lower the merged images.
Arrowheads indicate nuclei of the cells that express Lhx3. Open arrows indicate the constrictions in the row of nuclei of the lateral cells. Red dots indicate nuclei of the landmark cells.

Original annotation:
The first expression domain of Ci-Lhx3 consists of one cell, while the second domain contains five cells, including the L2, L3 and L4 cells on each side. In the gap between the two Ci-Lhx3 domains, there lies a single cell.
NB: All genes described in figure 4 are expressed exclusively in the lateral cell rows.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	lateral TNC ependymal cells - lateral VG ependymal cells -

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

Two-color-fluorescence WISH was performed at the late tailbud stage. Lhx3 expression is shown in red, vAChTP in green.

Original annotation:
Ci-Lhx3 is expressed in the visceral ganglion and part of the tail nerve cord. Expression of Ci-Lhx3 in the posterior CNS is detected in two domains with a narrow gap between them. The first domain of Ci-Lhx3 does not correspond to that of Ci-vAChTP.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	tail nerve cord - visceral ganglion -

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

Two-color-fluorescence WISH was performed at the late tailbud stage. Lhx3 expression is shown in red, Fgf8/17/18 in green.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	tail nerve cord - visceral ganglion -

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

Two-color-fluorescence WISH was performed at the late tailbud stage. Lhx3 expression is shown in green.

Original annotation:
Ci-Lhx3 is expressed in the visceral ganglion and in part of the tail nerve cord. The first domain of Ci-Lhx3 is locating between the third and fourth domain of Ci-SoxB1.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	tail nerve cord - visceral ganglion -

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

Late tailbud embryo probed for Ci-vAChTP expression (in blue), Ci-Lhx3 expression (in green) and Ci-SoxB1 expression (in red).

Original annotation:
According to the gene expression map (Ikuta and Saiga, 2007), expression of Ci-Lhx3 was observed in A13.474, A11.117 and A11.118 cell pairs.

Aniseed annotation:
Corresponding fate for these cells : lateral visceral ganglion.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	visceral ganglion -

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

Late tailbud embryo probed for Ci-vAChTP expression (in blue), Ci-Lhx3 expression (in green) and Ci-SoxB1 expression (in red) following the injection of Ci-Hox5-MO.

Original annotation:
Expression of the genes that share the expression domain with the Hox genes at tailbud or larval stage was unaffected in the tailbud embryos or larvae injected with MOs against Ci-Hox1, 2, 3, 4 and 5.

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	visceral ganglion -

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

Stained molecule	KH2012:KH.S215.4 (LHX3; LHX4; LHX5)
Stained region(s)	endoderm - tail muscles -