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 Nishikata T et al., Dev Biol. 2001; 238:315-331. Original annotation: mitochondrial-type. Expression pattern: Localized

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)	whole embryo -

Conversion to Aniseed format of Ghost database entry from Nishikata T et al., Dev Biol. 2001; 238:315-331. Original annotation: mitochondrial-type. Expression pattern: A4.1 a4.2 B4.1 b4.2

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)	whole embryo -

Lateral view of a gastrula stage wild type embryo hybridized with a riboprobe for a neural-specific isoform of ascidian tubulin, HrTBB2. (but which tubulin?)

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)	neural plate - tail muscles -

Lateral view of a mid neurula stage embryo treated with DMSO and probed for homolog of Tubulin beta 2 chain (cluster ID 00086r1).

Original annotation:
Expression in the brain, nerve cord and presumptive papilla cells. Expression was stronger in the anterior half of the brain (red arrow) than in the posterior half (blue arrow). Brackets show the presumptive papilla region.

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)	neural plate -

Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904.

Original annotation:
Expression pattern: Nerve cord Brain Papilla.
Comment : a pair of cells in the tip of the tail was especially strongly stained.

Aniseed annotation : a staining has been detected in the nervous system but also in the tail nerve cord, the visceral ganglion and the palps. A very strong staining has been detected in the tip of the tail epidermis.

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)	central nervous system -

Lateral view of an early tailbud stage wild type embryo hybridized with a riboprobe for a neural-specific isoform of ascidian tubulin, HrTBB2. (which tubulin?)

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)	central nervous system - tail epidermis -

Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904.

Original annotation:
Expression pattern: Nerve cord Brain Papilla Neuron.
Comment : a pair of cells in the tip of the tail was especially strongly stained.

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)	central nervous system -

Dorsal view of an early tailbud stage embryo treated with DMSO and probed for homolog of Tubulin beta 2 chain (cluster ID 00086r1).

Original annotation:
00086 cluster was expressed in the brain, nerve cord and the presumptive papilla. Arrowheads indicate presumptive papilla region. Red and blue arrows indicate the staining in the anterior and posterior regions of the brain, respectively.

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)	anterior sensory vesicle - neck - posterior sensory vesicle - tail nerve cord - visceral ganglion -

Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904.

Original annotation:
Expression pattern: Endodermal strand Nerve cord Brain Papilla.

Aniseed annotation :
Expression at the tip of the tail?

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)	central nervous system - head endoderm - posterior endodermal strand (B8.12 line) -

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)

Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904.

Original annotation:
Expression pattern: Endodermal strand Nerve cord Brain Papilla.

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)	central nervous system - endoderm -

Fluorescence image of late-tail bud stage embryos electroporated with a GFP fusion gene containing the 4336-bp Ci-tubulin-beta2 enhancer (construct named Ci-tubulin-beta2-EGFP(wt) in the paper). White arrows and arrowheads indicate GFP fluorescence in the brain and visceral ganglion respectively. Yellow arrows and arrowheads indicate GFP fluorescence in caudal epidermal neurons and the adhesive organ, respectively.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates in the paper : -4300bp/-1bp

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)	anterior sensory vesicle - caudal epidermal neurones (CEN) - posterior sensory vesicle - visceral ganglion -

Fluorescence image of late-tail bud stage embryos electroporated with a GFP fusion gene containing the 4336-bp Ci-tubulin-beta2 enhancer which the M2 site is mutated (construct named Ci-tubulin-beta2-EGFP(uM2) in the paper). White arrows and arrowheads indicate GFP fluorescence in the brain and visceral ganglion respectively. Yellow arrows and arrowheads indicate GFP fluorescence in caudal epidermal neurons and the adhesive organ, respectively.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.
Coordinates in the paper : -4300bp/-1bp

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)	anterior sensory vesicle - caudal epidermal neurones (CEN) - posterior sensory vesicle - visceral ganglion -

Conversion to Aniseed format of Ghost database entry from Kusakabe T et al., Dev Biol. 2002; 242:188-203. Original annotation: . Expression pattern: Endoderm Nervecord Brain Ganglion

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)	anterior sensory vesicle - head endoderm - neck - posterior sensory vesicle - tail nerve cord - visceral ganglion -

Conversion to Aniseed format of Ghost database entry from Ogasawara et al., Dev Genes Evol. 2002; 212:173-185. Original annotation: ubiquitous. Expression pattern: Endostyle Pharyngeal gill Heart Intestine Body wall muscle Neural gland Epidermis Stomach Esophagus

Stained molecule	KH2012:KH.L116.85 (TUBB; TUBB2B; TUBB4B)
Stained region(s)