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. 2022 Feb 17;11:e72825. doi: 10.7554/eLife.72825

Figure 5. Distinguishing mutation-dependent gene expression changes from allele-specific expression (ASE).

(A) Plot of normalised counts consistent with ASE. This shows either reduced expression from the allele on one of the wild-type chromosomes (white chromosome in the diagram under the plot) or increased expression from the allele on the t3 chromosome (red chromosome). Yellow = wild-types (+/+), orange = t3 heterozygotes (t3/+), blue = baz1 heterozygotes (+/baz1), purple = compound heterozygotes (t3/baz1). (B) Normalised counts consistent with a response to the sox10 mutations. The compound heterozygotes have reduced expression and the other two groups of heterozygotes are intermediate between the compound heterozygotes and the wild types. (C). Boxplots of the expression of all the differentially expressed (DE) genes on chromosome 3. These are split into two groups, those that are consistent with being downstream of sox10 (sox10-DE) and those that appear to be driven by allele-specific expression unrelated to sox10 (ASE-DE).

Figure 5—source data 1. Counts for polr3h.
Normalised counts for polr3h (ENSDARG00000102590) in sox10t3/baz1 incross at Prim-5 (24 hr post-fertilisation [hpf]).
Figure 5—source data 2. Counts for vasnb.
Normalised counts for vasnb (ENSDARG00000102565) in sox10t3/baz1 incross at Prim-5 (24 post-fertilisation [hpf]).
Figure 5—source data 3. Counts for the genes represented in Figure 5C.
Normalised counts for the genes represented by the boxplots in Figure 5C (sox10t3/baz1 incross at Prim-5/24 hr post-fertilisation [hpf]).

Figure 5.

Figure 5—figure supplement 1. Allele-specific expression not linked to the homozygous region.

Figure 5—figure supplement 1.

The expression of this gene according to genotype is not consistent with a response to a recessive mutation. Yellow = wild types (+/+), orange = t3 heterozygotes (t3/+), blue = baz1 heterozygotes (+/baz1), purple = compound heterozygotes (t3/baz1).