AmpliSeq™ libraries were constructed and sequenced on the Ion Torrent Proton platform (Thermo Fisher) according to the manufacturer’s instructions as previously described24 (link),25 (link). For human gene analysis in cell lines, the Ion AmpliSeq Transcriptome Human Gene Expression Kit is designed for targeted amplification of over 20,000 human RefSeq genes simultaneously in a single primer pool. A short amplicon (~110 bp) is amplified for each targeted gene. Since an AmpliSeq transcriptome mouse kit is not commercially available, an Ion AmpliSeq™ Custom Panel was designed by the manufacturer (Thermo Fisher) using Ion AmpliSeq™ Designer for targeted amplification of 3,826 mouse genes that are most relevant for our studies (one short amplicon for each gene) in one primer pool for mouse studies. For each sample, 10 ng of total RNA was used for cDNA library preparation. Multiple libraries were multiplexed and clonally amplified using the Ion OneTouch 2 System (Thermo Fisher), and then sequenced on an Ion Torrent Proton machine (Thermo Fisher). Data was first analyzed by Torrent Suite and ampliSeqRNA analysis plugin (Thermo Fisher) to generate count data.
Ion torrent proton machine
Manufactured by Thermo Fisher Scientific
The Ion Torrent Proton is a benchtop next-generation DNA sequencing system. It utilizes semiconductor-based sequencing technology to detect the release of hydrogen ions during DNA synthesis, which is then converted into digital sequence data. The Proton is capable of sequencing a wide range of nucleic acid sample types, including genomic DNA, transcriptomes, and targeted panels.
Automatically generated - may contain errors
Lab products found in correlation
Ion onetouch 2 system, by Thermo Fisher Scientific (2 mentions)
Torrent suite, by Thermo Fisher Scientific (2 mentions)
Ion ampliseq custom panel, by Thermo Fisher Scientific (2 mentions)
Ion ampliseq designer, by Thermo Fisher Scientific (2 mentions)
Ion torrent proton platform, by Thermo Fisher Scientific (2 mentions)
Ampliseqrna analysis plugin, by Thermo Fisher Scientific (2 mentions)
2 protocols using ion torrent proton machine
1
AmpliSeq Transcriptome Profiling for Cell Lines
2
AmpliSeq Transcriptome Profiling for Cell Lines
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AmpliSeq™ libraries were constructed and sequenced on the Ion Torrent Proton platform (Thermo Fisher) according to the manufacturer’s instructions as previously described24 (link),25 (link). For human gene analysis in cell lines, the Ion AmpliSeq Transcriptome Human Gene Expression Kit is designed for targeted amplification of over 20,000 human RefSeq genes simultaneously in a single primer pool. A short amplicon (~110 bp) is amplified for each targeted gene. Since an AmpliSeq transcriptome mouse kit is not commercially available, an Ion AmpliSeq™ Custom Panel was designed by the manufacturer (Thermo Fisher) using Ion AmpliSeq™ Designer for targeted amplification of 3,826 mouse genes that are most relevant for our studies (one short amplicon for each gene) in one primer pool for mouse studies. For each sample, 10 ng of total RNA was used for cDNA library preparation. Multiple libraries were multiplexed and clonally amplified using the Ion OneTouch 2 System (Thermo Fisher), and then sequenced on an Ion Torrent Proton machine (Thermo Fisher). Data was first analyzed by Torrent Suite and ampliSeqRNA analysis plugin (Thermo Fisher) to generate count data.
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