Journal: bioRxiv

Article Title: Development of Coupling Controlled Polymerizations by Adapter-ligation in Mate-pair Sequencing for Detection of Various Genomic Variants in One Single Assay

doi: 10.1101/400689

Figure Lengend Snippet: The first adapter (Ad1, blue) with/without a barcode sequence (indicated by grey bar) is ligated to genomic DNA fragments (black lines). Various adapter designs may be used as the first adapter [e.g., blunt-end adapters, Y-shaped Illumina adapters, bubble adapters ( Supplementary Fig. S2 ), etc.]. After Ad1 ligation and PCR, DNA ends are ligated together to form dsCirs containing a gap. naCNT is performed and results in DNA polymerization (dashed lines) and the movement of the gap into a selected length of the genomic DNA. 3’-branch ligation is used to ligate a 3’-end of the second adapter (Ad2_3’, yellow). The two strands of the dsCir are separated, and the single-stranded DNA (ssDNA) with Ad2_3’ at the 3’-end is used as a template for CPE (ntCPE or ttCPE). The Ad2_5’ sequence (green) is added to the 3’-end of the CPE product through 3’-branch ligation. After PCR, this results in genomic DNA with half of Ad2 at each end separated by Ad1.

Article Snippet: For all four libraries, single-stranded circles (ssCirs) and DNA nanoballs (DNBs) were prepared and subjected to improved cPAL (Combinatorial Probe-Anchor Ligation) sequencing on a DNA nanoball (DNB)-based sequencing platform [Complete Genomics, Inc., (CGI), Mountain View, CA, USA].

Techniques: Sequencing, Ligation

Journal: bioRxiv

Article Title: Development of Coupling Controlled Polymerizations by Adapter-ligation in Mate-pair Sequencing for Detection of Various Genomic Variants in One Single Assay

doi: 10.1101/400689

Figure Lengend Snippet: (A) Spectrum of chromosomal structural rearrangements. Each sample is indicated with the linkages with one particular color and the event stated next to the linkages. All events are illustrated by the data from CP-AL with paired-end 100 bp sequencing and validated by Sanger sequencing. The events missed by the data from the same sample using shorter read-lengths are indicated by the red arrows (26 bp) and blue arrows (50 bp, outmost), respectively. Chromosomal nucleotide positions and bands are shown according to the University of California, Santa Cruz Genome Viewer Table Browser. The compositions of original chromosomes and the derivation chromosomes illustrated by the sequencing data from CP-AL with paired-end 100 bp reads in Sample03 and Sample05 are shown in figure (B) and (C), respectively. Each DNA/chromosome segment is shown with a different color and an arrow indicating the genomic orientation.

Article Snippet: For all four libraries, single-stranded circles (ssCirs) and DNA nanoballs (DNBs) were prepared and subjected to improved cPAL (Combinatorial Probe-Anchor Ligation) sequencing on a DNA nanoball (DNB)-based sequencing platform [Complete Genomics, Inc., (CGI), Mountain View, CA, USA].

Techniques: Sequencing

Journal: bioRxiv

Article Title: Development of Coupling Controlled Polymerizations by Adapter-ligation in Mate-pair Sequencing for Detection of Various Genomic Variants in One Single Assay

doi: 10.1101/400689

Figure Lengend Snippet: (A) The compositions of normal chromosomes (shown in green dotted frame) and the derivation chromosomes (shown in red dotted frame) illustrated by the sequencing data from CP-AL with paired-end 100 bp reads in Sample 02. Each DNA/chromosome segment is shown with a different color and an arrow indicating the genomic orientation. (B) Visualization ( http://www.kobic.kr/3div/ ) of interaction between gene SLC17A5 and the other locations in PrEC normal Prostate epithelial cell, BglII, the most relevant cell line in the reported database. Bi. Distribution of topological associated domains (triangles in blue); Bii. Distributions of distance normalized interaction frequency and bias-removed interaction frequency; Biii. Present of super enhancers; Biv. Distribution of genes (RefSeq). The disruption location is indicated by red line ( SLC17A5 indicated by a red arrow), while the locations of the certain topological associated domain (same as SLC17A5 ) are shown in orange dotted lines. Black arrow and green indicate the super enhancer of gene EEF1A1 and the gene itself, respectively.

Article Snippet: For all four libraries, single-stranded circles (ssCirs) and DNA nanoballs (DNBs) were prepared and subjected to improved cPAL (Combinatorial Probe-Anchor Ligation) sequencing on a DNA nanoball (DNB)-based sequencing platform [Complete Genomics, Inc., (CGI), Mountain View, CA, USA].

Techniques: Sequencing, Disruption