A targeted, multiplex PCR primer panel was designed using the custom Ion AmpliSeq Designer v5.4.1 (Life Technologies, Carlsbad, CA, USA). The primer panel covered 42.21 kb of target regions that included potential mutations identified from MuTect1 software. Additionally, we also included two reported highly recurrent mutations in the NOTCH1 gene: (1) chr9: 139390648 (2) chr9: 139390152 (non-coding region); and mutations in the TP53, ATM, MYD88 and POT1 genes (coding region only). Design coverage of the intended targets was 98.9%. Average amplicon size of the 228 amplicons in the design was 242 bp. Sample DNA (30ng) was amplified using this custom AmpliSeq primer pool, and barcoded libraries were prepared for each sample following the manufacturer’s Ion AmpliSeq Library Preparation protocol (Life Technologies, Carlsbad, CA, USA). After library preparation, up to 96 libraries were pooled, templated and sequenced on the Proton Sequencer using the Ion P1 200bp Kit and the P1 chip per manufacturer’s instructions (Life Technologies, Carlsbad, CA, USA).
P1 chip
Manufactured by Thermo Fisher Scientific
Sourced in United States
The P1 chip is a high-throughput sequencing platform designed for DNA and RNA analysis. It provides a compact and efficient solution for generating large volumes of sequencing data. The P1 chip is capable of producing accurate and reliable sequencing results, making it a versatile tool for a wide range of applications in genomics research and molecular diagnostics.
Automatically generated - may contain errors
2 protocols using p1 chip
1
Targeted multiplex PCR for mutation detection
2
Sequencing Desiccated Nostoc Genome
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An environmental sample of desiccated Nostoc, after storage at −25°C for 16 years, was ground in liquid nitrogen. DNA was extracted with a Nucleospin kit (Macherey-Nagel) using lysis buffer PL2 and sent to the Nevada Genomics Center (NGC) at the University of Nevada Reno for sequencing. A library was prepared using the Ion Xpress Plus fragment library kit (Life Technologies) and sequenced on an Ion Torrent Proton platform using Hi-Q chemistry and a P1 chip (Life Technologies), yielding about 86.1 million reads with an average length of 181 bp. The reads were assembled into 877,292 contigs (average length, 702 bp) with CLC Genomics Workbench, with a total length of about 616 million bp.
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