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The "barcode" is an eight-base sequence unique to each sample.
The reverse primer contains a 6-bp error-correcting barcode unique to each sample.
While the two samples shared some common peaks, the spectra were different, with some peaks unique to each sample.
DNA was amplified by using the 515f/806r primer set (515f: 5′-GTG CCAGCMGCCGCGGTA A-3′, 806r: 5′-XXX XXXGGGTWTCTA GGGTWT CTA AT-3′), which targets the V4 region of the microbial 16S rRNA, whichtargetserse primer conthening a 6-bp error-correcting barcode unique to each sample.
The method relies on cutting DNA with a chosen restriction enzyme, ligating an adapter containing a molecular identifying sequence (MID) unique to each sample, and sequencing the DNA associated with each restriction site using the massively parallel Illumina sequencing technology [10].
In addition, we assumed that footprint sites would be unique to each sample.
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We also generate a UPGMA tree using $SC MESQUITE $ESC:[ 103] based on pairwise distances calculated using an F84 model of nucleotide substitution [ 104] using haplotypes unique to each sampling site.
The adapters contain a 5-bp "index" sequence that is unique to each individual sample.
Next, we removed the peaks shared by control and Dex-exposed cells, so that the remaining peaks were unique to each specific sample, and referred to as DMRs.
Libraries were then amplified with primers to incorporate a unique index to each sample.
cDNA construction and attachment of unique barcodes to each sample ensued (Illumina Inc, San Diego CA).
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