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).

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

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
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 :Atonal.
Expression pattern : No distinct zygotic signal was detected

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
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 :Atonal.
Expression pattern : No distinct zygotic signal was detected.

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
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 :Atonal.
Expression pattern : No distinct zygotic signal was detected.

Aniseed annotation:
According to the picture, a staining might have been detected but it remains unsure.

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
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 :Atonal.
Expression pattern : No distinct zygotic signal was detected.

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
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 :Atonal.
Expression pattern : No distinct zygotic signal was detected.

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
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 :Atonal.
Expression pattern : No distinct zygotic signal was detected.

Aniseed annotation:
According to the picture, we can detect staining in the tail muscles area but it's more likely to be an artefact.

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
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 :Atonal.
Expression pattern : No distinct zygotic signal was detected.

Aniseed annotation:
According to the pictures, unidentifiable staining have been detected but it's more likely to be artefact.

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
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 :Atonal.
Expression pattern : No distinct zygotic signal was detected.

Aniseed annotation:
According to the pictures, unidentifiable staining have been detected but it's more likely to be artefact.

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
Stained region(s)	No expression -

Lateral view of an early tailbud stage embryo stained with Atonal.
Original annotation: No expression was observed in the embryo.
Aniseed annotation: According to the pictures, unidentifiable staining have been detected : artefact or palps ?

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
Stained region(s)

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 :Atonal.
Expression pattern : nervous system, nerve cord.
Comment : epidermal neurons, parts of the brain, papilla

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
Stained region(s)	caudal epidermal neurone (CEN) precursors - rostral trunk epidermal neurone precursors (RTEN) (a8.26 line) -

Lateral view of a mid tailbud stage embryo stained with Atonal. White lines demarcate boundaries between different focal planes.
Original annotation: Expression was observed in epidermal sensory neurones.

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
Stained region(s)	apical trunk epidermal neurone precursors (ATEN) - caudal epidermal neurone (CEN) precursors - rostral trunk epidermal neurone precursors (RTEN) (a8.26 line) -

Lateral view of a late tailbud stage embryo stained with Atonal. White lines demarcate boundaries between different focal planes.
Original annotation: Expression was observed in epidermal sensory neurones.

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
Stained region(s)	apical trunk epidermal neurones (ATEN) - caudal epidermal neurones (CEN) - rostral trunk epidermal neurones (RTEN) -

Dorasl view of a Ciona robusta larva micro-injected with Asic1b>CFP(green) and Atonal >Kaede (red) reporter constructs.
Asic1 cis-regulatory region drives CFP expression in the sensory vesicle and visceral ganglion in the trunk and in bipolar neurons of the tail (BTNs).
Scale bars = 100μm.

Stained molecule	KH2012:KH.C1.215 (ASIC1; ASIC2; ASIC3)
Stained region(s)	anterior bipolar tail epidermal neurones (b8.18 line) - anterior sensory vesicle - posterior bipolar tail epidermal neurones (b8.21 line) - posterior bipolar tail epidermal neurones (b8.25 line) - posterior sensory vesicle - visceral ganglion -

Dorasl view of a Ciona robusta larva micro-injected with Asic1b>CFP(green) and Atonal >Kaede (red) reporter constructs.
Atonal cis-regulatory region drives Kaede expression in palps neurons, rostral trunk epidermal neurons (RTENs), anterior and posterior apical trunk epidermal neurons (aATENs and pATENs), Caudal epidermal neurons (CESNs) and bipolar tail neurons (BTNs).
Original annotation: This Atoh1/Atonal/lin‐32 reporter is active in nearly all sensory neurons, including CESNs, consistent with previous in situ hybridization results (Joyce Tang, Chen, & Zeller,2013). Interestingly, Atonal is expressed in BTNs.
Scale bars = 100μm.

Stained molecule	KH2012:KH.C8.175 (ATOH1; ATOH7; NEUROD1)
Stained region(s)	anterior bipolar tail epidermal neurones (b8.18 line) - apical trunk epidermal neurones (ATEN) - caudal epidermal neurones (CEN) - palp neurones - posterior bipolar tail epidermal neurones (b8.21 line) - posterior bipolar tail epidermal neurones (b8.25 line) - rostral trunk epidermal neurones (RTEN) -