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Plates were developed using 3,3',5,5'-Tetramethylbenzidine 3,3',5,5'-Tetramethylbenzidineously described[ 12].
In one Methanosarcinale, Mathenosaeta thermophila, only a partial PylS sequence was identified from a short sequence read, as previously noted [ 20].
The BinaxNOW S. pneumoniae urinary antigen test (Inverness Medical Diagnostics, Princeton, NJ, USA) was performed and read as previously described (11 ).
ChIP tracks were plotted by taking strand-shifted reads (covering 200 nt from original read start) and computing overlaps for the center 100 nt of each read, as previously described (Arvey et al., 2014).
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For constitutive junctions and retention of constitutive introns the isoform ratios were estimated using junction-spanning reads, as previously described [ 17].
In the third pipeline we performed a de novo assembly with Trinity on the unmapped reads as previously described, however we increased the length of the contigs to >200 bp.
Then, the 27 amplicons of the complete TET2 coding region (n = 24) were sequenced using 454 FLX amplicon deep-sequencing chemistry with a median coverage of 689 reads, as previously described [ 17, 18].
For a pair of HLA alleles, we then iterate through each base position and multiply the probabilities of observing the base genotypes unique to these HLA alleles given the 454 sequence reads as previously calculated by the GATK.
Fragment libraries of CHA, 491, PT22 and TB63741 were sequenced with the Illumina Genome Analyser II generating 36 bp reads as previously reported for strains TBCF10839 and TBCF121838 [ 16].
At variant positions, deviation from the most common nucleotide was rare, in most cases and did not exceed 1% of the reads, as previously observed in 454 sequence data.
To further compare the small RNA expression profiles between virus-infected plants and mock-infected plants, we performed extensive BLAST searches to map all small RNA sequences to the Arabidopsis genome (Table 1), except for siRNAs derived from the viral genome which were 210 reads (12.4 % of total reads), as previously reported.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com