Ordered aggregates can extend into β-strand enriched fibrils, regardless of their initial native conformational states.
We found positivity for those probes specifically recognizing L-strand, thus demonstrating that this strand is enriched, while H strand did not (Supplementary Fig. S4).
Since ChIP-DNA fragments are equally likely to be sequenced from both ends, the tag density around a true binding site should show a bimodal enrichment pattern, with forward strand tags enriched upstream of binding sites and reverse strand tags enriched downstream of binding sites [ 10, 11, 35, 37].
For example, whereas TAS2 3'D6 siRNA strand is enriched in infected tissues, the complementary strand (TAS2 3'D6 of the ta-siRNA duplex is not.
The other strand is enriched for As since the Crick strand's un-methylated Cs become Ts, which are complemented with As.
This revealed a number of locations on each strand highly enriched for uniquely mapping reads.
Notice that one strand is enriched for Ts since the PCR and bisulfite treatment converts unmethylated Cs to Ts.
CH > TH substitutions (i.e. C > T mutations on the H strand) were enriched for the Np CpG trinucleotide context (8- to 15-fold more frequent than expected by chance; Figure 3A).
Small RNAs of between 26-29 nthatat derived from the antisense strand of TEs generally (>70% of all sequences) showed a strong enrichment for U at their 5' end (U1-bias), while those derived from the sense strand are enriched for A at position 10 (A-10 bias).
In all chromosomes except Sakl0C-left, lagging strands are enriched in G over C and in T over A bases, whereas leading strands are enriched in C and A bases.
A signal-processing algorithm (see Statistical Methods Supplement) was utilized to analyze the microarray data and to identify peaks indicating the positions on the genome where short nascent DNA strands were enriched.
