PMC:6218809 / 11179-12301 JSONTXT

{"project":"2_test","denotations":[{"id":"30388403-19505943-2049232","span":{"begin":674,"end":676},"obj":"19505943"}],"text":"Illumina Sequencing of DUP4 Samples\n1 μg genomic DNA was randomly fragmented to a size of 350 bp by shearing, DNA fragments were end polished, A-tailed, and ligated with the NEBNext adaptor for Illumina sequencing, and further PCR enriched by P5 and indexed P7 oligos. The PCR products were purified (AMPure XP system) and the resulting libraries were analyzed for size distribution by an Agilent 2100 Bioanalyzer and quantified using real-time PCR.\nFollowing sequencing on an Illumina platform, the resulting 150 bp paired-end sequences were examined for sequencing quality, aligned using BWA to the human reference genome (hg19 plus decoy sequences), sorted using samtools35 and duplicate reads marked using Picard, generating the final bam file. Sequencing and initial bioinformatics was done by Novogene Ltd.\nSequence read depth was calculated using samtools to count mapped reads in non-overlapping 5 kb windows across the glycophorin region. Read counts were normalized for coverage to a non-CNV region (chr4:145516270–145842585), then to the first 50 kb of the glycophorin region which has diploid copy number of 2."}