Libraries were constructed using a custom paired-end protocol (Illumina) (Falconer et al. 2012 (link)). Briefly, samples were end-repaired and A-tailed, and Illumina PE adapters were ligated. Libraries were amplified using indexed PE primers for eight to 10 PCR cycles. Amplified indexed libraries were pooled (four to six libraries per pool) and size-selected for paired-end sequencing. A detailed library construction procedure is presented in the Supplemental Material. Cluster generation and paired-end sequencing (100-base-pair [bp] reads) were performed on the Illumina cluster station and Illumina HiSeq 2000 sequencing platform. Sequence reads were mapped to mm9 (NCBI 37) using BWA (Li and Durbin 2009 (link)). Reads passing Illumina’s default chastity filter (Li et al. 2009 (link)) were used to generate library statistics.
Protocol detail
Illumina-Based Paired-End Sequencing Protocol
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Base pair
Library
Primers
Corresponding Organization :
Other organizations : University of British Columbia, Kyushu University, Japan Science and Technology Agency, RIKEN
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Variable analysis
independent variables
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- Samples were end-repaired and A-tailed, and Illumina PE adapters were ligated.
- Libraries were amplified using indexed PE primers for eight to 10 PCR cycles.
- Amplified indexed libraries were pooled (four to six libraries per pool) and size-selected for paired-end sequencing.
- Cluster generation and paired-end sequencing (100-base-pair [bp] reads) were performed on the Illumina cluster station and Illumina HiSeq 2000 sequencing platform.
- Sequence reads were mapped to mm9 (NCBI 37) using BWA (Li and Durbin 2009).
- Reads passing Illumina's default chastity filter (Li et al. 2009) were used to generate library statistics.
- None explicitly mentioned
- None explicitly mentioned
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