Table 1. List of genes and CRMs that showed comparable responses to the perturbations.

Perturbation	dnCad MOE (80 pg/µl)	HesC MASO (100 µM)	Nodal MASO (100 µM)	Nodal MOE (80 pg/µl)	SoxB1 MASO (100 µM)	Total
Gene (CRMs)a	16 (20)b	1 (1)	2 (3)	8 (10)	3 (6)	30 (40)
	blimp1b* (bP)c, chordin (U3), eve (2.1k), ficolin (I1), foxa* (I), gatae (m10), gcm (E), lim1 (I1), nodal (5P, INT), otxb1/2 (m06), prox1 (U1), tbrain (C), univin (U1, I1-2), wnt8 (A, B, C), z13 (U1), z188 (I2)	delta (R6)	chordin (U3), nodal (5P, INT)	bmp2/4 (U2, U3), chordin (U3), gatac (U2), gcm (E), gsc (U1), nk2.2 (U1-3), nodal (5P, INT), not (U1)	ficolin (I1, I2), nodal (5P, INT), otxb1/2 (m6, m16)

dnCad MOE, dominant negative cadherin mRNA over expression; HesC MASO, translation blocking MASO against hesc; Nodal MASO, translation blocking MASO against nodal; Nodal MOE, nodal mRNA over expression; SoxB1 MASO, translation blocking MASO against soxb1. Concentration or molarity of each reagent injected is shown under the name of each reagent.

^aGenes and CRMs (within parenthesis) up regulated by the perturbation are shown in italic type and those down regulated in roman type.

^bNumbers of genes and CRMs (within parenthesis) responded in the perturbation are shown.

^cGenes and CRMs with known cis-regulatory information are underlined, and genes with asterisks (*) means that we failed capturing CRMs with known cis-regulatory information; blimp1b and eve [24], foxa [23], wnt8 [26], delta [27], and nodal [14].