We again tested if these patterns changed with varying stringencies of defining pathogenic ncSNVs and with gene clustering patterns, yielding similar findings (Supplementary Figs. 8-10).
We compared the profile of putative VTA DA neurons with those recorded using the DA reporter mouse line PITX3-GFP53 yidenticaldentical profiles (Supplementary Fig. 6).
The above analyses were also calculated after excluding ceiling performers on the attentional task (five control subjects and one patient), yielding similar results (Supplementary material).
We tested four different dictionary sizes (k = 100, 200, 500 and 1000), all yielding similar results (Supplementary Material), and we report later in the text results for k = 500, which obtained slightly higher accuracies.
18 non-overlapping cellular features reflecting nuclear, cytoplasm and ciliary state, combined into 31 parameters (Supplementary file 1), yielding 559,395 values across the screen (Supplementary file 2).
A BEM (provided as Supplementary Dataset) was constructed from the deleterious somatic mutations derived from this dataset (as detailed in the Supplementary Materials), yielding 757 rows (i.e. samples), 9757 columns (i.e. genes), 19 758 non-null entries (i.e. variants), corresponding to an edge density equal to 0.27% in the corresponding bipartite network.
To obtain successive generations of SlIAA9-crispr mutants effectively, artificial crossing of the SlIAA9 mutant and wild-type is an important process in yielding the seedless phenotype (Supplementary Fig. 5b).
For further stringency, confounding probesets were removed (Supplementary Material), yielding 88 464 sets with a median of 18 probes.
We selected Refseq genes with significant differential expression over the time course (FDR < 0.05, SAMseq) and varied by at least twofold, yielding 3690 significant transcripts (Supplementary file 1F).
AfS77 was transformed with two DNA fragments each containing overlapping but incomplete fragments of the pyrithiamine resistance-conferring gene ptrA as described previously (Schrettl et al, 2010) yielding strain Δ hapX (Supplementary Fig S7A).
Second, the finding is not an artifact of a single symbiont genome (Vtu) being poorly sequenced and yielding apparent elevated nonsynonymous substitution rates (supplementary fig. S3, Supplementary Material online).
