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Table 1 Optimized conditions for PacBio-LITS library preparation

From: PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations

Experimental conditions Library insert sizes
1 Kb 4 Kb 6 Kb 7-8 Kb
Input DNA 500 ng 1 μg 1.5 μg 2 μg
Shearing method Covaris Covaris or g-TUBE g-TUBE g-TUBE
Shearing condition 1 Kb shearing with microTube Covaris: 5 Kb shearing with miniTube or g-TUBE: 12000 rpm, 45 sec. 7000 rpm, 3 min. 4800 rpm, 8 min.
Size selection method Pippin Blue Pippin Blue Pippin Blue Pippin
Size selection condition Range mode: 900 bp-1.3 Kb Range mode: 4 Kb-8 Kb Range mode: 5 Kb-9 Kb Range mode: 8 Kb-12 Kb
DNA Polymerase Phusion HF Polymerase TaKaRa LA Taq Polymerase (Hot-start) TaKaRa LA Taq Polymerase (Hot-start) TaKaRa LA Taq Polymerase (Hot-start)
Pre-cap PCR cycle # 6 8 8 10
DNA amount into Capture 1 μg 1 μg 2 μg 2 μg
Post-cap PCR cycle # 14 16 16 18
Mean mapped subread length ~700 bp ~1.8-2 Kb ~2-2.5 Kb ~2.5-3 Kb
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