Figure 1.
A schematic representation of the CLIP-PE library construction strategy.
Following fragmentation, the DNA molecules are end-repaired and ligated with LoxP-P1 and LoxP-P2 adaptors integrated with Illumina P1 or P2 sequences. After separation and size selection, DNA is circularized by Cre recombinase, and non-circularized DNA is removed by exonuclease digestion. bp enzyme cutter is then used to digest and fragment DNA. (Alternatively, circularized DNA can be fragmented by random shearing to 400–500 bp followed by end-repair). DNA is then self-ligated. Inverse PCR with Illumina P1 and P2 PCR primers is used to enrich the mate paired molecules for sequencing. The final prepared libraries consist of short fragments made up of two DNA segments that were originally separately by 5–22 kb.
Table 1.
Results from the alignment of Haloterrigena turkmenica VKM, DSM 5511 5 kb mate pair libraries made with CLIP-PE method and Illumina Jumping method to the reference genome.
Figure 2.
Histogram of insert lengths from the Haloterrigena turkmenica VKM, DSM 5511 5 kb mate pair libraries.
A: CLIP-PE method, B: Illumina jumping method. The distribution of insert lengths was determined by aligning the reads to the reference genome.
Figure 3.
Histogram of insert sizes from Saccharomyces cerevisiae Illumina 12 kb CLIP-PE libraries.
The distribution of insert lengths was determined by aligning the reads to the reference genome.
Table 2.
Results from the alignment of Saccharomyces cerevisiae Illumina 12 kb CLIP-PE libraries to the reference genome.
Table 3.
Results from the alignment of Saccharomyces cerevisiae Illumina 22 kb CLIP-PE libraries to a reference genome.
Figure 4.
Histogram of insert sizes from Saccharomyces cerevisiae Illumina 22 kb CLIP-PE libraries.
A: cut with NlaIII, B: cut with HpyCh4IV, C: random shearing approach. The distribution of insert lengths was determined by aligning the reads to the reference genome.
Figure 5.
Assembly metrics for Saccharomyces cerevisiae Illumina CLIP-PE libraries.
std refers to standard Illumina 250 bp library, sim 12 kb refers to simulated 12 kb mate pair library, and sim 22 kb refers to simulated 22 kb mate pair library.
Table 4.
Mis-assembly numbers of Saccharomyces cerevisiae CLIP-PE libraries.