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)

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16) Gene name: Y-box protein1/2/3.

Original annotation:
Expression pattern: Unlocalized signal was detected.
Comment : Ubiquitous staining was observed throughout embryogenesis. This expression is likely maternal.

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	whole embryo -

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 :Y-box protein1/2/3.
Expression pattern : Unlocalized signal was detected

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	whole embryo -

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16) Gene name: Y-box protein1/2/3.

Original annotation:
Expression pattern: No zygotic signal was detected.
Comment : Ubiquitous staining was observed throughout embryogenesis. This expression is likely maternal.

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	whole embryo -

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16) Gene name: Y-box protein1/2/3.

Original annotation:
Expression pattern: No zygotic signal was detected.
Comment : Ubiquitous staining was observed throughout embryogenesis. This expression is likely maternal.

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	whole embryo -

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 :Y-box protein1/2/3.
Expression pattern : No distinct zygotic signal was detected

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	No expression -

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16) Gene name: Y-box protein1/2/3.

Original annotation:
Expression pattern: No zygotic signal was detected.
Comment : Ubiquitous staining was observed throughout embryogenesis. This expression is likely maternal.

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	whole embryo -

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 :Y-box protein1/2/3.
Expression pattern : No distinct zygotic signal was detected

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	No expression -

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16) Gene name: Y-box protein1/2/3.

Original annotation:
Expression pattern: No zygotic signal was detected.
Comment : Ubiquitous staining was observed throughout embryogenesis. This expression is likely maternal.

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	whole embryo -

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 :Y-box protein1/2/3.
Expression pattern : No distinct zygotic signal was detected

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	No expression -

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16) Gene name: Y-box protein1/2/3.

Original annotation:
Expression pattern: No zygotic signal was detected.
Comment : Ubiquitous staining was observed throughout embryogenesis. This expression is likely maternal.

Aniseed annotation :
According to the picture, a signal have been detected in the B8.15 and B8.16 cell pairs. A signal might have been detected in the B7.7, A8.5, A8.6, A8.7, A8.8, A8.13 and A8.15 cell pairs.

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	A8.13 cell pair - A8.15 cell pair - A8.5 cell pair - A8.6 cell pair - A8.7 cell pair - A8.8 cell pair - B7.7 cell pair - B8.15 cell pair - B8.16 cell pair -

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 :Y-box protein1/2/3.
Expression pattern : No distinct zygotic signal was detected

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	No expression -

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 :Y-box protein1/2/3.
Expression pattern : muscle

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	tail muscles -

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

Original annotation :Gene name: Y-box protein1/2/3.
Expression pattern: muscle.
Comment : Ubiquitous staining was observed throughout embryogenesis. This expression is likely maternal.

Aniseed annotation :
In addition to few cells in the tail muscles, few cells in the nervous system are stained.

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	neural plate - tail muscles -

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16) Gene name: Y-box protein1/2/3.

Original annotation :
Expression pattern: muscle.
Comment : Ubiquitous staining was observed throughout embryogenesis. This expression is likely maternal.

Aniseed annotation :
A very strong staining has been detected in the tail muscles and in the nervous system.

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	neural plate - tail muscles -

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 :Y-box protein1/2/3.
Expression pattern : muscle

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	tail muscles -

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 :Y-box protein1/2/3.
Expression pattern : muscle, nervous system

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	nervous system - tail muscles -

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16) Gene name: Y-box protein1/2/3.

Original annotation:
Expression pattern: muscle nervous system.
Comment : Ubiquitous staining was observed throughout embryogenesis. This expression is likely maternal.

Aniseed annotation :
In addition to a very strong staining detected in the tail muscles, a weaker staining has been detected in the central nervous system. A weak staining might have been detected in the palps.

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	central nervous system - tail muscles -

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 :Y-box protein1/2/3.
Expression pattern : muscle, nervous system

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	nervous system - tail muscles -

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

Original annotation:
Gene name: Y-box protein1/2/3.
Expression pattern : muscle nervous system.
Comment : Ubiquitous staining was observed throughout embryogenesis. This expression is likely maternal.

Aniseed annotation :
In addition to a very strong staining detected in the tail muscles, a weaker staining has been detected in the central nervous system. A weak staining might have been detected in the palps and the trunk ventral cells.

Stained molecule	KH2012:KH.C1.264 (YBX1; YBX2; YBX3)
Stained region(s)	central nervous system - tail muscles - trunk ventral cells (B7.5 line) -