Supplementary specifications regarding inclusion profiles and studies belonging to CIMBA are available in the reports by Couch et al. [ 35] and Gaudet et al. [ 36].
There is a 24-gene overlap between our 96-gene signature and that of Hoek et al., with 18 of the genes in common, including MITF, involved in melanin biosynthesis, pigmentation, development, and lineage specification (Supplementary Information S1), which reinforces the importance of these pathways in melanoma.
We found that concentrations lower than 50 ng/ml activin A did not markedly influence mesoderm specification (supplementary material Fig. S2).
Importantly, we also observed a significant increase in expression of the canonical Wnt/β-catenin inhibitor DKK1 in anterior-derived cardiogenic mesoderm, which suggests a more repressive state of Wnt/β-catenin signaling during cardiac specification (supplementary material Fig. S3B).
Pairwise comparison of RNA-Seq results between these cell populations at E15.5 and E18.5 revealed an increase in the expression of a number of genes important for β-cell specification (supplementary material Tables S4 and S5).
In order to provide a human- and machine-readable format that is able to properly represent and analyze pathways, and with the feature of being compliant with the SBGN specifications, we developed a data format based on the SBGN Process Definition (PD) 1.1 specification (Supplementary Material).
Furthermore, expression of RFP in the Tg ifabp:RFP) as200 transgenic line and neutral red uptake was unchanged, indicating normal intestinal bulb and mid intestinal specification (supplementary material Fig. S5B and S5C, respectively) (Flores et al., 2008; Oehlers et al., 2011a).
See Supplementary methods for specifications of the microscope and image acquisition.
The overall recovery was 65%, and endotoxin and host cell protein levels were within specifications (Supplementary Methods).
Sensitivity analyses assessed the stability of the results to the model specification (see supplementary file).
