All the custom analysis scripts used for this project are available at https://github.com/davidaknowles/dox (Knowles and Blischak, 2017). The suez response eQTL mapping R package is available at https://github.com/davidaknowles/suez (Knowles, 2017). The following data are available as Supplementary Data: 1) differential expression cluster assignments, 2) significant (5% FDR) eQTLs and sQTLs, 3) differential splicing results, 4) levels of cardiac troponin and the predicted transcriptomic response. In addition to the Supplementary Data included with this paper, further results are hosted at Dryad (doi:10.5061/dryad.r5t8d04) including 1) gene-by-sample matrix of RNA-seq quantification (log counts per million), 2) LeafCutter intron excision quantification 3) p-values for all tested eQTLs, reQTLs, sQTLs, and rsQTLs, 4) RARG variant response and marginal trans-eQTLs, 5) RIN, RNA concentration and other technical covariates, 6) embryoid body imaging for all iPSC lines. The RNA-seq FASTQ files will be added to the dbGaP database (Tryka et al., 2014) under dbGaP accession phs000185 (https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000185). The genotype data files cannot be shared because releasing genotype data from a subset of individuals in the pedigree would enable the reconstruction of genotypes of other members of the pedigree, which would violate the original protocol approved by the research ethics board (Livne et al., 2015). The summary statistics for the ACT GWAS were given to us by the authors of the study (Schneider et al., 2016; Serie et al. 2017).

The following data sets were generated:

Knowles DACourtney K BurrowsJohn D BlischakCarole OberJonathan K PritchardYoav Gilad (2018) Expression and splicing quantification, eQTLs and sQTLs Available at Dryad Digital Repository under a CC0 Public Domain Dedication. http://dx.doi.org/10.5061/dryad.r5t8d04

Courtney K BurrowsKnowles DAJohn D BlischakKristen M PattersonCarole OberJonathan K PritchardYoav Gilad (2018) Genetic Studies in the Hutterites Available at dbGaP via dbGaP Authorized Access (accession no. phs000185.v5.p1). https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000185

© 2018, Knowles et al.

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