DNA reads of the mitochondrial fraction (100-250 nt in length, supplementary table S2, Supplementary Material online) were assembled with Newbler (GS De Novo Assembler v.2.9).
Based on domain architecture, the subtypes a (short), b ("long" with only DUF3751), and c (long with DUF3751 and PF07484) are distinguished, which can be further differentiated by AA sequence and length (supplementary table S3, Supplementary Material online).
Overall, these correlations, which were largely unchanged when controlling for sequence length (supplementary table S6, Supplementary Material online), suggest remarkable concordance between the patterning of DNA methylation, when present, and histone modifications across evolutionary time (Nanty et al. 2011).
Percentages of nucleotide differences were calculated over the validated sequence length (supplementary fig. S2, Supplementary Material online).
These stem-loop structures tend to reside in intergenic regions, and 20 have stems predicted to be >40 bp in length (supplementary fig. S2, Supplementary Material online).
In contrast, AsmA proteins show more diversity regarding sequence length (supplementary fig. S3, Supplementary Material online), and the AsmA domain covers either the entire protein or only the N-terminal region (supplementary fig. S4, Supplementary Material online).
Nevertheless, a greater than linear relationship between the pol β indel error rate and repeat number was observed for [GT] motifs of 6 13 units in length (supplementary fig. S4 A, Supplementary Material online).
This result was highly significant for all data sets (Mann–Whitney test P < 10−4), and it resulted from both a larger number of indels and a larger mean indel length (supplementary file S2: table S3, Supplementary Material online).
We confirmed a significant reduction in both dendritic length (Supplementary Fig. 8g, h) and branch number (Supplementary Fig. 8g, i) in EGFP+ DGCs from Oxtr f/f mice with AAV-Cre-GFP injections compared with those injected with AAV-GFP.
Correspondingly, digestion with SmaI digestion produced longer restriction fragments and the signal of both TTTTAGG- and Chlamydomonas-type probes was distributed among multiple BAL31-sensitive fragments of 2.5 23 kb length (supplementary fig. S3 B, the bottom panel, Supplementary Material online).
We also used discordant mapping of paired ends to reveal structural variants (SVs) of at least 20 bp in length (Supplementary Note).
