Additional file 1 of Tropomyosin 1 genetically constrains in vitro hematopoiesis

Additional file 1:Table S1. The 860 chromatin feature tracks included in our LASSO analysis. These data were obtained from ENCODE [68], ChromHMM [81], and analyses of primary human MK cells [26]. Table S2. Chromatin features and coefficients comprising our penalized regression-based platelet scoring model. Coefficients for background parameters are included at the bottom of this list, but were not included in subsequent genome-wide SNP scoring. Table S3. Gene Ontology pathways that were significantly enriched in the top 1% of SNPs, as defined by platelet model scores. Presented pathways had false discovery rate (FDR) < 5%. Table S4. Gene Ontology pathways that were significantly enriched in the top 1% of SNPs, as defined by GWAVA scores. Presented pathways had false discovery rate (FDR) < 5%. Table S5. Gene Ontology pathways that were significantly enriched in the top 1% of SNPs, as defined by CADD scores. Presented pathways had false discovery rate (FDR) < 5%. Table S6. CRISPR/Cas9-edited Tropomyosin 1 knockout (KO) iPSC lines did not incur any additional CNVs compared to the parent line. Analyses of wild type CHOP14 and CHOP10 ‘parent’ lines, and derivative TPM1KO ‘child’ lines, are shown. Karyotype and copy number variation (CNV) analyses for all child lines were consistent with parental iPSC lines. Table S7. Dysregulated molecular pathways in TPM1KO MKs. FACS-sorted MKs were analyzed by microarray, and gene set enrichment was performed. Upregulated Gene Ontology [30] pathways with FDR<25% are shown. There were no significantly downregulated pathways. GO, Gene Ontology. NES, nominal enrichment score. FDR, false discovery rate. Table S8. Chromatin features and coefficients comprising our penalized regression-based red cell scoring model. Coefficients for background parameters are included at the bottom of this list, but were not included in subsequent genome-wide SNP scoring. Table S9. Gene Ontology pathways that were significantly enriched in the top 1% of SNPs, as defined by red cell model scores. Presented pathways had false discovery rate (FDR) < 5%. Table S10. Penalized regression-based fine-mapping identifies eQTLs in established platelet and/or red cell trait GWAS loci that overlie GATA binding sites. Listed SNPs are within platelet or red cell trait GWAS LD blocks (EUR r2>0.7), scored in the top 5% by both our platelet trait and red cell models, overlap canonical or near-canonical GATA binding sites, and are eQTLs for at least 1 gene [41] (GTEx V7). Associated GWAVA [17] scores are present, if available. SNP rsIDs and locations refer to hg19 genome. Table S11. Semi-quantitative RT-PCR primers used in this study.