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)

Stained molecule	KH2012:KH.C8.280 (KH.C8.280)
Stained region(s)	a8.17 cell pair - a8.18 cell pair - a8.19 cell pair - a8.20 cell pair - b8.17 cell pair - b8.18 cell pair - b8.19 cell pair - b8.20 cell pair -

Reporter expression of the region upstream of ELK was detected in the precursors of central nervous system, muscles, notochord and epidermis.

Stained molecule	KH2012:KH.C8.280 (KH.C8.280)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - a8.17 cell pair - a8.19 cell pair - B7.1 cell pair - B7.2 cell pair - B7.7 cell pair - B8.15 cell pair - b8.18 cell pair - b8.20 cell pair -

Views of mid-gastrula stage embryos showing expression of ELK when the gene is regulated by the region: Ci-ELK-c Scaffold_3:780955-781272.

Stained molecule	KH2012:KH.C8.280 (KH.C8.280)
Stained region(s)	No expression -

Reporter expression of the region upstream of ELK was detected in the precursors of central nervous system, muscles, notochord and epidermis.

Stained molecule	KH2012:KH.C8.280 (KH.C8.280)
Stained region(s)	endoderm - epidermis - neural plate - notochord - tail muscles -

ELK expression was detected in the brain (sensory vesicle), the nerve cord, the palps, muscles, notochord, endoderm and endodermal strand epidermis (midline).

Stained molecule	KH2012:KH.C8.280 (KH.C8.280)
Stained region(s)	anterior sensory vesicle - endoderm - epidermis - notochord - posterior sensory vesicle - tail muscles - tail nerve cord -

Views of early tailbud stage embryos showing expression of ELK when the gene is regulated by the region: Ci-ELK-c Scaffold_3:780955-781272.

A weak signal was sometimes detected in mesenchyme and in notochord.

Stained molecule	KH2012:KH.C8.280 (KH.C8.280)
Stained region(s)	notochord -

Original annotation: very weak expression.

Aniseed annotation:
Data and annotation provided by the author, not available in the article.

Stained molecule	KH2012:KH.C8.280 (KH.C8.280)
Stained region(s)	trunk ventral cells (B7.5 line) -

Views of mid-tailbud stage embryo showing expression of ELK when the gene is regulated by the region: Ci-ELK-b Scaffold_3:779266-780043.

As we can see on the second picture, rarely there is a weak signal in mesenchyme.

Stained molecule	KH2012:KH.C8.280 (KH.C8.280)
Stained region(s)	No expression -

Dorsal (2nd picture) and lateral (last picture) views of a tailbud embryo showing reporter expression of a region of ELK.

Original Annotation : Reporter expression of Elk was detected in mesenchyme, b-epidermis (mid-line), nerve cord and b-muscle.

ANISEED Annotation : Acording to the pictures it seems that there is no nerve cord staining.

Stained molecule	KH2012:KH.C8.280 (KH.C8.280)
Stained region(s)	posterior dorsal midline head epidermis (b8.20 line) - posterior most secondary muscle lineage (b8.17 line) -

Views of larvae showing expression of ELK when the gene is regulated by the region: Ci-ELK-c Scaffold_3:780955-781272.

A weak signal was detected in mesenchyme and in notochord.

Stained molecule	KH2012:KH.C8.280 (KH.C8.280)
Stained region(s)	notochord -

Views of an embryo showing reporter expression of the region upstream of Ci-ELKa.

Original Annotation : Staining was detected in the mesenchyme, b-epidermis (mid line), nerve cord, and b-muscle.

ANISEED Annotation : According to the pictures there is no staining in the muscle or in the nerve cord.

Stained molecule	KH2012:KH.C8.280 (KH.C8.280)
Stained region(s)	posterior dorsal midline head epidermis (b8.20 line) -

Views of larvae showing expression of ELK when the gene is regulated by the region: Ci-ELK-b Scaffold_3:779266-780043.

As we can see in the picture there is sometimes weak staining in the mesenchyme.

Stained molecule	KH2012:KH.C8.280 (KH.C8.280)
Stained region(s)	No expression -

Reporter expression of the region upstream of Elk was detected in the central nervous system, muscles, notochord, endoderm and epidermis.

ANISEED Annotation : According to the pictures it seems that there is also staining in the mesenchyme.

Stained molecule	KH2012:KH.C8.280 (KH.C8.280)
Stained region(s)	central nervous system - endoderm - epidermis - notochord - tail muscles -