Table 1 A breakdown outline for the steps used for sequencing HCC tissue samples
From: Genomic landscape of hepatocellular carcinoma in Egyptian patients by whole exome sequencing
No | Step | Kit | Manufacture | Instrument |
|---|---|---|---|---|
1 | DNA Extraction | QIAamp DNA mini Kit | Qiagen | –- |
2 | Measure concentration of DNA (QC Step) | Qubit dsDNA HS assay | ThermoFisher Scientific | Qubit 3.0 |
3 | Amplify the targets | Ion AmpliSeqâ„¢ Exome RDY Kit /Â Ion Xpressâ„¢ Barcode Adapters | ThermoFisher Scientific | 9700 Thermal Cycler |
4 | Partially digest amplicons | |||
5 | Ligate barcoded adapters to the amplicons | |||
6 | Purify the unamplified library | Agencourtâ„¢ AMPureâ„¢ XP Reagent | Beckman Coulter | DynaMagâ„¢-2 Magnet |
7 | Quantify the library | Ion Library Taqman Quantitation Kit | ThermoFisher Scientific | Viia 7 Real Time PCR |
8 | Template preparation, loading chips and sequencing | Ion PIâ„¢ Hi-Qâ„¢ Chef Kit | Ion Torrent | Ion Chef |
9 | Ion PIâ„¢ Chip | Ion Proton |