(a) Multiple short oligonucleotide probes each containing a SNP unique to the maternal or paternal allele are labeled with distinct dyes (b) Representative maximum intensity z-projections of Alexa 594 (top) and Cy5 (bottom), for cells that only express the variant in the 129 strain (left), only the Castaneus variant (middle), and both (right). Each strain-specific set contains 29 probes complementary to the x-chromosomal gene Yipf6. We circled computation identified spots and inferred true signal (solid), and noise (dashed) from the known absence or presence of the transcript type in each cell line. Scale bars, 5 µm.

(a) Scatter plot of the quantified relative intensities of Alexa 594 and Cy5 for Rlim transcripts in cells that only express either the 129 transcript variant (magenta) or only the Castaneus transcript variant (green). The grey dashed line is the manual segmentation for allele-assignment. (b) The average correct assignments rates for Nanog (12 probes), Rlim (13 probes), Yipf6 (29 probes), and Fat1 (39 probes) quantified using (orange) and without using (blue) information from the “identification” channel. Data was averaged over n = 4 biological replicates, with 2 experiments each for cells expressing only Castaneus transcripts and cells expressing only 129 transcripts (except for Fat1 for which we lack an exclusively Castaneus expressing cell line). Error bars, 1 s.e.m. (c) Scatter plots of allele-specific Nanog mRNA expression for cells grown under serum and 2i conditions. (d) The distribution of bright transcription sites for Nanog in cells grown under serum and 2i conditions. (e) Box plots of allele-specific Nanog mRNA counts sorted according to the presence (on) or absence (off) of a bright transcription site for cells grown in 2i. Whiskers, 2.7 s.d. P values, Wilcoxon rank sum test. (f) Scatter plots for cells grown in 2i for all combinations of Nanog expressed from either the 129 allele or the Castaneus allele, and Chd4 expressed from either the 129 allele or the Castaneus allele.