We use solution nuclear magnetic resonance spectroscopy to directly probe the dynamic architecture within FUS liquid phase-separated assemblies.
Multivalent interactions are likely to contribute to the dynamic, liquid-like properties of phase separated unimolecular assemblies [ 47, 48], as well as of more complex assemblies [ 46, 49].
Interactions relevant to the phase separation phenomenon occur over multiple length scales, from sub-nanometer to tens of micrometers, thereby making any single analytical technique insufficient for the study of phase separated macromolecular assemblies.
We performed separated Velvet assemblies 9 of the different sequencing runs, and found the presence of the Leucobacter DNA in a single experiment (SRR065714), consisting of 8,887,206 single reads of 76 bp.
The GAM program) [ 67] combined separate assemblies produced by the CLC and ABySS assemblers [ 8, 68].
The reads were assembled in three combinations, resulting in three separate assemblies of fox transcriptome: i) assembly of all sequencing reads from both samples; ii) assembly of sequencing reads from the sample of tame fox; iii) assembly of sequencing reads from the sample of aggressive fox.
In the separate assemblies, the genes with high expression levels (ESM1, rbcS) were assembled to a full length transcript in most assemblies.
TopHat alignments were assembled into transcripts using Cufflinks 2.1.1 [ 60], generating three separate assemblies, one for each library.
For each strain and assembler, n = 27 (SOAPdenovo) or n = 10 (AbySS) separate assemblies were produced, in each case iterating K from 31 to 81.
The three separate assemblies for N. tabacum, N. sylvesteris and N. tomentosiformis transcripts were further assembled using GsAssembler.
Their competitive assembly ranked 2nd overall, and was produced by the Metassembler tool [ 55] which combined the results of two separate assemblies (CSHL* and CSHL**, that were made using the Allpaths and SOAPdenovo assemblers respectively).
