SRX3892921 GSM3082824 SRP137709 SRS3130728 GSM3082824 OTHER TRANSCRIPTOMIC other Upon mixing the 50-60 million BOBSC iPS cells with the DT40 cells (10:1 ratio) , the nuclear fraction was extracted (then treated with rnaseH for the control), genomic DNA containing containing DNA:RNA hybrid purified, soluble contaminating RNA was digested with RNase I, sonicated to average size of 300 bp with Bioruptor Diagenodtreatments and immunoprecipitated DNA:RNA hybrids with S9.6 antibody. Following low, high, LiCl and TE buffer washes of Protein-G captured immunocomplexes, DNA:RNA hybrids were eluted, phenol:chloroform purified, denatured for 5 minutes at 95 C, DNA moity digested with DNaseI, and RNA moiety of the DNA:RNA hybrid purified with Trizol. Directional RNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7645) per instructions provided. Steps from random priming to End Prep of cDNA was followed as instructed in for rRNA depleted FFPR RNA samples, and further steps where followed as instructed for purified mRNA or rRNA depleted RNA. Illumina HiSeq 4000 gds 303082824 GSM3082824 GEO Accession GSM3082824 SRX3892922 GSM3082825 SRP137709 SRS3130729 GSM3082825 OTHER TRANSCRIPTOMIC other Upon mixing the 50-60 million BOBSC iPS cells with the DT40 cells (10:1 ratio) , the nuclear fraction was extracted (then treated with rnaseH for the control), genomic DNA containing containing DNA:RNA hybrid purified, soluble contaminating RNA was digested with RNase I, sonicated to average size of 300 bp with Bioruptor Diagenodtreatments and immunoprecipitated DNA:RNA hybrids with S9.6 antibody. Following low, high, LiCl and TE buffer washes of Protein-G captured immunocomplexes, DNA:RNA hybrids were eluted, phenol:chloroform purified, denatured for 5 minutes at 95 C, DNA moity digested with DNaseI, and RNA moiety of the DNA:RNA hybrid purified with Trizol. Directional RNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7645) per instructions provided. Steps from random priming to End Prep of cDNA was followed as instructed in for rRNA depleted FFPR RNA samples, and further steps where followed as instructed for purified mRNA or rRNA depleted RNA. Illumina HiSeq 4000 gds 303082825 GSM3082825 GEO Accession GSM3082825 SRX3892923 GSM3082826 SRP137709 SRS3130730 GSM3082826 OTHER TRANSCRIPTOMIC other Upon mixing the 50-60 million BOBSC iPS cells with the DT40 cells (10:1 ratio) , the nuclear fraction was extracted (then treated with rnaseH for the control), genomic DNA containing containing DNA:RNA hybrid purified, soluble contaminating RNA was digested with RNase I, sonicated to average size of 300 bp with Bioruptor Diagenodtreatments and immunoprecipitated DNA:RNA hybrids with S9.6 antibody. Following low, high, LiCl and TE buffer washes of Protein-G captured immunocomplexes, DNA:RNA hybrids were eluted, phenol:chloroform purified, denatured for 5 minutes at 95 C, DNA moity digested with DNaseI, and RNA moiety of the DNA:RNA hybrid purified with Trizol. Directional RNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7645) per instructions provided. Steps from random priming to End Prep of cDNA was followed as instructed in for rRNA depleted FFPR RNA samples, and further steps where followed as instructed for purified mRNA or rRNA depleted RNA. Illumina HiSeq 4000 gds 303082826 GSM3082826 GEO Accession GSM3082826