Additional file 2.

Figure S1. RainDance Genomic DNA Template Droplet and Primer Droplet Merge. PCR droplets are generated on the RDT 1000 instrument (RainDance Technologies, Inc. USA). For a single sample, the gDNA template mix and the RainDance 384 Member Primer Library and four consumables are required, namely RDT 1000 Chip, RDT 1000 Template input/output vial, RDT 1000 Collect input/output vial, and a PCR Tube Strip, Axygen Scientific. The RDT 1000 instrument generated each PCR droplet by pairing a single gDNA template droplet with a single primer droplet. The paired droplets flow past an electrode embedded in the chip and are instantly merged creating the PCR droplet. All of the resulting PCR droplets were automatically dispensed as an emulsion into a single PCR tube and transferred to a standard thermal cycler for PCR amplification. Figure S2. A and B Comparison of DNA Fragment Distribution of RainDance 384 Member Primer Panel BioAnalyzer Trace with RainDance 384 Member Primer Library Predicted Amplicon Profile. Comparisons of the DNA fragment distribution of RainDance 384 Member Primer Panel Bioanalyzer Trace (2A) with the predicted profile (2B). As shown here, the amplicon profile obtained from the Agilent Bioanalyzer results (2A) nicely matches the predicted histogram distribution (2B). Figure S3. Removal of Primer-Dimer Peaks Using Agencourt AMPure Kit. (A) A typical electropherogram obtained showed a primer-dimer peak between 60 and 70 bp (~ 68 bp). B) The primer-dimer peak (and other unincorporated dNTPs, primers, salts and other contaminants) were removed after purification of the SOLiD Fragment Library (here Library 759L is shown as an example) using the standard procedure of Agencourt AMPure Kit (Beckman Coulter Genomics). Figure S4. Coverage Uniformity Across all the Barcoded and Pooled Samples Before (pB) and After (pA) Emulsion PCR. A comparable distribution of average depth of coverage (ADoC) across libraries pooled before and after emulsion PCR (emPCR) is shown here. Barcoded libraries pooled after emPCR (792 (pA)), showed more uniform ADoC. Samples assigned to barcode 4 (yellow point) showed the lowest ADoC.

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ElSharawy et al. BMC Genomics 2012 13:500   doi:10.1186/1471-2164-13-500