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Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library		1 clone(s) / 5,577
Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult		16 clone(s) / 31,366
Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo		4 clone(s) / 15,579
Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg		0 clone(s) / 31,100
Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva		6 clone(s) / 26,704
Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo		7 clone(s) / 26,680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K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis		0 clone(s) / 5,468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Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells		1 clone(s) / 29,579
Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle		0 clone(s) / 2,556
Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo		11 clone(s) / 16,939
Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula		8 clone(s) / 25,258
Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad		0 clone(s) / 16,936
Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex		5 clone(s) / 10,463
Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart		1 clone(s) / 13,243
Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland		0 clone(s) / 17,765
Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal		2 clone(s) / 17,872
Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal		6 clone(s) / 107,314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		1 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)		28 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

61 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 :SoxB1.
Expression pattern : No signal was detected.

Aniseed annotation :
No picture from Ghost data.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
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 :SoxB1.
Expression pattern : A5.1, A5.2, a5.3, a5.4, b5.3, b5.4

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	A5.1 cell pair - A5.2 cell pair - a5.3 cell pair - a5.4 cell pair - b5.3 cell pair - b5.4 cell pair -

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

Animal view of late 16-cell stage embryo probed for SoxB1 expression.
Original annotation : Expression of Ci-SoxB1 was examined by WISH. The cleavage-stage embryos were imaged from the animal side. The anterior end is toward the top.Ci-SoxB1 is expressed at the 16–64 cell stage

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	a5.3 cell pair - a5.4 cell pair - A line - b5.3 cell pair - b5.4 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 :SoxB1.
Expression pattern : A6.1, A6.2, A6.3, A6.4, a6.5, a6.6, a6.7, a6.8, b6.5, b6.6, b6.7, b6.8

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	A6.1 cell pair - A6.2 cell pair - A6.3 cell pair - A6.4 cell pair - a6.5 cell pair - a6.6 cell pair - a6.7 cell pair - a6.8 cell pair - b6.5 cell pair - b6.6 cell pair - b6.7 cell pair - b6.8 cell pair -

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

Animal view of 32-cell stage embryo probed for SoxB1 expression.
Original annotation : Expression of Ci-SoxB1 was examined by WISH. The cleavage-stage embryos were imaged from the animal side. The anterior end is toward the top.Ci-SoxB1 is expressed at the 16–64 cell stage

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	A6.1 cell pair - A6.2 cell pair - A6.3 cell pair - A6.4 cell pair - a6.5 cell pair - a6.6 cell pair - a6.7 cell pair - a6.8 cell pair - b6.5 cell pair - b6.6 cell pair - b6.7 cell pair - b6.8 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 :SoxB1.
Expression pattern : A7.1, A7.2, A7.3, A7.4, A7.5, A7.6, A7.7, A7.8, a7.9, a7.10, a7.11, a7.12, a7.13, a7.14, a7.15, a7.16, b7.9, b7.10, b7.11, b7.12, b7.13, b7.14, b7.15, b7.16

Stained molecule

KH2012:KH.C1.99 (SOX14; SOX2; SOX21)

Stained region(s)

a7.10 cell pair - a7.11 cell pair - a7.12 cell pair - a7.13 cell pair - a7.14 cell pair - a7.15 cell pair - a7.16 cell pair - A7.1 cell pair - A7.2 cell pair - A7.3 cell pair - A7.4 cell pair - A7.5 cell pair - A7.6 cell pair - A7.7 cell pair - A7.8 cell pair - a7.9 cell pair - b7.10 cell pair - b7.11 cell pair - b7.12 cell pair - b7.13 cell pair - b7.14 cell pair - b7.15 cell pair - b7.16 cell pair - b7.9 cell pair -

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

Animal view of 64-cell stage embryo probed for SoxB1 expression.
Original annotation : Expression of Ci-SoxB1 was examined by WISH. The cleavage-stage embryos were imaged from the animal side. The anterior end is toward the top.Ci-SoxB1 is expressed at the 16–64 cell stage

Stained molecule

KH2012:KH.C1.99 (SOX14; SOX2; SOX21)

Stained region(s)

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 :SoxB1.
Expression pattern : A7.6, A8.7, A8.8, A8.15, A8.16, a8.17, a8.18, a8.19, a8.20, a8.21, a8.22, a8.23, a8.24, a8.25, a8.26, a8.27, a8.28, a8.29, a8.30, a8.31, a8.32, b8.18, b8.20, b8.21, b8.22, b8.23, b8.24, b8.25, b8.26, b8.27, b8.28, b8.29, b8.30, b8.31, b8.32

Stained molecule

KH2012:KH.C1.99 (SOX14; SOX2; SOX21)

Stained region(s)

A8.11 cell pair - A8.12 cell pair - A8.15 cell pair - A8.16 cell pair - a8.17 cell pair - a8.18 cell pair - a8.19 cell pair - a8.20 cell pair - a8.21 cell pair - a8.22 cell pair - a8.23 cell pair - a8.24 cell pair - a8.25 cell pair - a8.26 cell pair - a8.27 cell pair - a8.28 cell pair - a8.29 cell pair - a8.30 cell pair - a8.31 cell pair - a8.32 cell pair - A8.7 cell pair - A8.8 cell pair - b8.18 cell pair - b8.20 cell pair - b8.21 cell pair - b8.22 cell pair - b8.23 cell pair - b8.24 cell pair - b8.25 cell pair - b8.26 cell pair - b8.27 cell pair - b8.28 cell pair - b8.29 cell pair - b8.30 cell pair - b8.31 cell pair - b8.32 cell pair -

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

Late gastrula stage wild type embryo probed for SoxB1 expression. No picture available in the article.

Original Annotation :
SoxB1 was expressed in A9.13, A9.14, A9.15, A9.16, A9.29, A9.30, A9.32, b9.37 and b9.38 cell pairs.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	A9.13 cell pair - A9.14 cell pair - A9.15 cell pair - A9.16 cell pair - A9.29 cell pair - A9.30 cell pair - A9.32 cell pair - b9.37 cell pair - b9.38 cell pair -

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

ventral view of a mid gastrula embryo probed for SoxB1 expression (pseudocolored in magenta). Nuclei are shown by DAPI (green)
Original annotation : Expression of Ci-SoxB1 was examined at 5.5 hpf by FISH. The embryos were imaged from the ventral side with the anterior end toward the right.
The graph shows quantified expression level : The expression of SoxB1 along the A-P axis was quantified from the image. Normalized fluorescence intensities averaged along the D-V axis are shown for different embryos as line plots of different colors. The black-line plots represent the intensity quantified in the FISH image (a.u., arbitrary units).

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	whole embryo -

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.C1.99 (SOX14; SOX2; SOX21)

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 - b9.33 cell pair - b9.37 cell pair - b9.38 cell pair - dorsal midline anterior tail epidermis - dorso lateral head epidermis - lateral anterior tail epidermis - lateral posterior tail epidermis - ventral head epidermis -

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 :SoxB1.
Expression pattern : endoderm, epidermis, unidentifiable.
Comment : not expressed in the neural plate.

Aniseed annotation : a staining has been detected in the whole embryo but also in the endoderm and the epidermis.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	whole embryo -

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

Original annotation:
Staining not detected.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	No expression -

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 :SoxB1.
Expression pattern : endoderm, epidermis, unidentifiable.

Aniseed annotation : a staining has been detected in part of the endoderm and in the mesenchyme.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	endoderm -

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: Neuron

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	anterior sensory vesicle - tail nerve cord -

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: . Expression pattern: Neuron

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	anterior sensory vesicle -

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

Dorsal views of early tailbud stage embryo expressing SoxB1. The upper panel shows WISH signals, the middle DAPI signals and the lower the merged images.
Arrowheads indicate nuclei of the cells that express SoxB1. 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 expression of Ci-SoxB1 around the junction of the trunk and the tail comprises two distinct domains.IN the first domain, only a single cell expresses Ci-SoxB1 and the second domain contains two cells on each side.
NB: All genes described in figure 4 are expressed exclusively in the lateral cell rows.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	lateral TNC ependymal precursors - lateral VG ependymal precursors -

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

Lateral view of an early tailbud stage wild type embryo probed for SoxB1 expression.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	anterior sensory vesicle - head endoderm - tail nerve cord -

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

Lateral view of a tailbud stage embryo probed for SoxB1 expression following egg micro-injection of a Otx MO.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	central nervous system - head endoderm -

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

Lateral view of a early tailbud stage embryo probed for SoxB1 expression following egg micro-injection of a FoxA-a MO.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	No expression -

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

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

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	central nervous system - endoderm - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis -

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 :SoxB1.
Expression pattern : nervous system, nerve cord, endoderm.
Comment : expressed in the anterior brain and three pairs of domains in the nerve cord.

Aniseed annotation : a staining has been detected in the nervous system but also in part of the tail nerve cord. A staining has been detected in the endoderm but also in part of the head endoderm.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - tail nerve cord -

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

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

Original annotation:
Ci-SoxB1 is expressed in head endoderm and in part of tail nerve cord. the first domain of Ci-SoxB1 overlaps with the posterior part of the second domain of Ci-En.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - tail nerve cord -

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

Two-color fluorescence WISH was performed at the early tailbud stage. SoxB1 expression is shown in green, Hox1 in red.

Original annotation:
Ci-SoxB1 is expressed in head endoderm and in part of tail nerve cord. The second domain of Ci-SoxB1 overlaps with the anterior part of the second domain of Ci-Hox1.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - tail nerve cord -

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

Two-color fluorescence WISH was performed at the early tailbud stage. SoxB1 expression is shown in green, Hox5 in red.

Original annotation:
Ci-SoxB1 is expressed in head endoderm and in part of tail nerve cord. Ci-Hox5 is expressed just posterior to the second domain of Ci-SoxB1.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - tail nerve cord - 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 SoxB1 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 :
SoxB1 was expressed in A11.119 cell pair (anterior visceral ganglion), in A11.116 cell pair (lateral nerve cord) and in b10.76 cell pair (dorsal nerve cord).

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	dorsal TNC ependymal precursors (capstone cells) - lateral TNC ependymal precursors - visceral ganglion -

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

Dorsal view of an early tailbud stage embryo probed for SoxB1 expression, following the injection of neurogenin MO.
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 was lost (white arrow).

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	No expression -

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

Views of early tailbud stage embryos showing reporter expression of the region from -505bp to -215bp upstream of Ci-SoxB1 in all ectodermal cells.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	ectoderm -

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

Views of early tailbud stage embryos showing reporter expression of the region upstream of Ci-SoxB1 from -505bp to -215bp and drived by the Fog promoter.

Expression was very weak and detected in mesenchyme.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)

C. robusta formely Ciona int. type A, Stage 20 (early tailbud II)

Lateral view of the motor ganglion of a WT Ciona robusta early tailbud embryo probed for SoxB1 expression (green) and electroporated with FGF8/17/18>mCherry reporter construct (red).
SoxB1 is expressed in A11.119 motor neuron precursor (arrowhead) and in A9.29 progeny.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei).

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	visceral ganglion -

C. robusta formely Ciona int. type A, Stage 20 (early tailbud II)

Lateral view of the motor ganglion of a Ciona robusta early tailbud embryo probed for SoxB1 expression (green) and electroporated with FGF8/17/18>mCherry reporter construct (red) and FGF8/17/18>Su(H)-DBM overexpression construct.
SoxB1 expression is lost in A11.119 (unfilled arrowhead), but remains in A9.29 progeny.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red nuclei).

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	visceral ganglion -

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: Neuron

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)

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

Dorsal views of mid tailbud stage embryo expressing SoxB1. The upper panel shows WISH signals, the middle DAPI signals and the lower the merged images.
Arrowheads indicate nuclei of the cells that express SoxB1. 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-SoxB1 is expressed in a single cell in the first and second domains, respectively, on each side. The cell between the two domains corresponds to the M1 cell. Ci-SoxB1 is expressed in at least four cells in the anteriorz-most nerve cord.
NB: All genes described in figure 4 are expressed exclusively in the lateral cell rows.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	lateral TNC ependymal precursors - lateral VG ependymal precursors -

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

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

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	central nervous system - endoderm - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis -

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

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

Original annotation:
Ci-SoxB1 is expressed in head endoderm, visceral ganglion and part of tail nerve cord. The first domain of Ci-SoxB1 is immediately posterior to the second domain of Ci-En and the second domain of Ci-SoxB1 overlaps with the anterior part of the third domain of Ci-En.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - 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. SoxB1 expression is shown in green, Dmbx in green.

Original annotation:
Ci-SoxB1 is expressed in head endoderm, part of visceral ganglion and part of tail nerve cord. The Ci-Dmbx domain is located between these two expression domains of Ci-SoxB1.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - 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. SoxB1 expression is shown in green, Hox1 in red.

Original annotation:
Ci-SoxB1 is expressed in head endoderm, part of visceral ganglion and part of tail nerve cord. The expression domain of Ci-SoxB1 in the anterior nerve cord is included by the second domain of Ci-Hox1, which expands more posteriorly without distinct boundary.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - 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. SoxB1 expression is shown in red, Fgf8/17/18 in green.

Original annotation:
Ci-SoxB1 is expressed in head endoderm, part of visceral ganglion and part of tail nerve cord. Ci-Fgf8/17/18 is expressed just behind the second domain of Ci-SoxB1.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - 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. SoxB1 expression is shown in red Lhx3 in green.

Original annotation:
Ci-SoxB1 is expressed in head endoderm, part of visceral ganglion and part of 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.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - tail nerve cord - 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 :SoxB1.
Expression pattern : nervous system, nerve cord, endoderm.

Aniseed annotation : a staining has been detected in the tail nerve cord, the anterior sensory vesicle and in part of the head endoderm.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	anterior sensory vesicle - head epidermis - tail nerve cord -

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

Lateral view of a mid tailbud stage wild type embryo probed for SoxB1 expression.

Original annotation:
SoxB1 expression in the visceral ganglion was detected in A12.240 and A12.238 cell pairs.

Aniseed annotation:
According to the picture and other data in Aniseed, there is also expression in the tail nerve cord, in the sensory vesicle and in the head endoderm.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	anterior sensory vesicle - head endoderm - 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 SoxB1 expression, following the injection of SoxB1 MO.

Original annotation:
Expression was more strong and extended (black arrow).

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	anterior sensory vesicle - head endoderm - tail nerve cord - visceral ganglion -

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: Neuron

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	anterior sensory vesicle -

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

Dorsal views of late tailbud stage embryo expressing SoxB1. The upper panel shows WISH signals, the middle DAPI signals and the lower the merged images.
Arrowheads indicate nuclei of the cells that express SoxB1. 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, second, third and fourth expression domain of Ci-SoxB1 in the posterior trunk consist of one, one, two, and one cells, respectively.
NB: All genes described in figure 4 are expressed exclusively in the lateral cell rows.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	lateral TNC ependymal cells - lateral VG ependymal cells -

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

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

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	central nervous system - endoderm - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis -

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

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

Original annotation:
Ci-SoxB1 is expressed in head endoderm, in part of sensory vesicle, neck, visceral ganglion and tail nerve cord. At this stage, the expression of Ci-SoxB1 was detected in four domains in the posterior trunk CNS. The first and third domains coincide with the first and third domains of Ci-En, respectively and the second domain overlaps with the posterior-most part of the second domain of Ci-En.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	anterior sensory vesicle - head endoderm - neck - posterior sensory vesicle - 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. SoxB1 expression is shown in green, Dmbx in red.

Original annotation:
Ci-SoxB1 is expressed in head endoderm, part of sensory vesicle, neck, visceral ganglion and tail nerve cord. At this stage, the expression of Ci-SoxB1 was detected in four domains in the posterior trunk CNS. Ci-Dmbx is expressed between the second and third domains of Ci-SoxB1.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	anterior sensory vesicle - head endoderm - neck - 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. SoxB1 expression is shown in green, Hox1 in red.

Original annotation:
Ci-SoxB1 is expressed in head endoderm, sensory vesicle, visceral ganglion, neck and tail nerve cord. Expression of Ci-Hox1 and Ci-SoxB1 overlap in nervous system.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - neck - posterior sensory vesicle - 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. SoxB1 expression is shown in red, Fgf8/17/18 in green.

Original annotation:
Ci-SoxB1 is expressed in head endoderm, sensory vesicle, visceral ganglion, neck and part of tail nerve cord. Signal for Ci-Fgf8/17/18 is located between the third and fourth domains of Ci-SoxB1.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	anterior sensory vesicle - head endoderm - neck - posterior sensory vesicle - 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. SoxB1 expression is shown in red, Lhx3 in green.

Original annotation:
Ci-Lhx3 is expressed in head endoderm, neck, sensory vesicle and part of tail nerve cord. The first domain of Ci-Lhx3 is locating between the third and fourth domain of Ci-SoxB1.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	anterior sensory vesicle - head endoderm - neck - posterior sensory vesicle - 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. SoxB1 expression is shown in green, Hox3 in red.

Original annotation:
Ci-SoxB1 is expressed in head endoderm, sensory vesicle, neck, visceral ganglion and part of tail nerve cord. The second domain of Ci-Hox3 coincides with the third domains of Ci-SoxB1.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	anterior sensory vesicle - head endoderm - neck - posterior sensory vesicle - tail nerve cord - visceral ganglion -

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

Lateral view of the motor ganglion of a WT Ciona robusta late tailbud embryo probed for SoxB1 expression.
SoxB1 is expressed in A12.240, A12.238 and A13.473
Original comment: In control Ciona embryos, SoxB1 expression is seen in three non-neuronal cells of the MG, including A12.240 (filled arrowhead).

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	visceral ganglion -

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

Lateral view of the motor ganglion of a Ciona robusta late tailbud embryo probed for SoxB1 expression (red) and treated with the MEK inhibitor U0126 from the initial tailbud II stage.
SoxB1 is expressed in A12.238 and A13.473
Original comment: Late U0126 treatment (11 hpf) abolishes SoxB1 in A12.240 (unfilled arrowhead).

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	visceral ganglion -

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

Original annotation:
Staining detected in the anterior brain.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	anterior sensory vesicle -

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

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

Original annotation:
According to the gene expression map (Ikuta and Saiga, 2007), expression of Ci-SoxB1 was observed in A13.245, A12.240, A13.459, A13.460, A13.461, A13.462, A13.463, A13.464, A13.476 and A13.475 cell pairs.

Aniseed annotation:
These cells have several fates corresponding to lateral visceral ganglion and lateral visceral ganglion.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - lateral TNC ependymal cells - visceral ganglion -

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

Late tailbud embryo probed for Ci-Dmbx expression (in blue), Ci-En expression (in green) and Ci-SoxB1 expression (in red) following the injection of Ci-Hox3-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.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - lateral TNC ependymal cells - 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).

Aniseed annotation:
These cells have several fates corresponding to lateral visceral ganglion and lateral visceral ganglion.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - lateral TNC ependymal cells - 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.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	head endoderm - lateral TNC ependymal cells - visceral ganglion -

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

Views of larvae showing reporter expression of the region upstream of Ci-SoxB1 from -1911bp to -1541bp and drived by the Fog promoter.

Weak expression was sometimes detected in mesenchyme.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)

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

Views of larvae showing reporter expression of the region upstream of SoxB1 in all ectodermal cells.

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)	ectoderm -

C. robusta formely Ciona int. type A, Stage 48 (young adult)

Conversion to Aniseed format of Ghost database entry from Ogasawara et al., Dev Genes Evol. 2002; 212:173-185. Original annotation: . Expression pattern: Pharyngeal gill

Stained molecule	KH2012:KH.C1.99 (SOX14; SOX2; SOX21)
Stained region(s)