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A set of 5 μg fluorescent-labeled cRNA targets from each sample was assembled into a hybridisation reaction on the Mouse Oligo Microarray (Agilent Technologies) using the In Situ Hybridization Kit Plus (Agilent Technologies).
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Between 2.22 and 7.35 Gbp of trimmed data from each sample was assembled independently.
Each sample was assembled in ABySS using every 5th kmer ranging from 26bp to 96bp.
The trimmed reads derived from each sample were assembled using velvet v1.12/oases v1.15 [ 37] and tgicl/CAP3 [ 38].
Unmapped reads of each sample were assembled independently from the reference.
Failed samples were assembled into a new plate and amplified with matK_390f and matK_1326r [ 51].
The study sample was assembled from lists provided by The Human Resources Departments.
More than 48,755,516 HQ reads from a cDNA library generated that was assembled into 43,891 unigenes.
These resultant unigene datasets from each sample were then assembled into a unique "All-unigene sequence" dataset using the TGICL platform.
Sequences from PCR products were assembled into the shotgun assemblies using CodonCode Aligner-v3.7.1 (CodonCodeCorp., USA).
Archived myocardial samples obtained during autopsy from 1995 to 2009 were assembled into four groups: RA; scleroderma; fatal myocarditis; and non-rheumatic disease controls.
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