Library construction and target gene enrichment were performed using the SureSelect XT Target Enrichment system (Agilent technologies Inc.), according to the manufacturer’s instructions based on a published protocol [24 (link)]. In short, the fractionated genomic DNA (3 μg) was end-repaired, 3′ dA overhangs added followed by adapter ligation. Between the three library generation steps, the samples were purified and concentrated, using AMPureXP bead system (1.8x volume beads), washed twice in 70% ethanol (Agencourt Bioscience Corporation) and eluted in nuclease-free water. The libraries were finally amplified (12 cycle protocol), using Hercules II fusion PCR system (Agilent Inc.) and purified again with AMPureXP bead system. Libraries were quantified, using Nanodrop 1000 (Thermo Fisher Inc.).
Ampurexp bead system
Manufactured by Agilent Technologies
Sourced in United States
The AMPure XP bead system is a nucleic acid purification tool used for the selective isolation and concentration of DNA or RNA fragments from complex samples. The system utilizes paramagnetic beads to reversibly bind nucleic acids, allowing for efficient washing and elution steps. This automated process enables the purification of target molecules from PCR, sequencing, and other molecular biology applications.
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Lab products found in correlation
Sureselectxt target enrichment system, by Agilent Technologies (1 mentions)
Hercules 2 fusion pcr system, by Agilent Technologies (1 mentions)
Hiseq 2000 platform, by Illumina (1 mentions)
Poly t oligo attached magnetic beads, by Thermo Fisher Scientific (1 mentions)
Nebnext adaptor oligonucleotides, by Illumina (1 mentions)
Neb universal pcr primer and index primer, by Illumina (1 mentions)
Klenow exo, by Illumina (1 mentions)
Truseq pe cluster kit v3 cbot hs, by Illumina (1 mentions)
2 protocols using ampurexp bead system
1
SureSelect XT Target Enrichment Protocol
2
RNA-seq library preparation and sequencing
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mRNA was purified from total RNA using poly-T oligo-attached magnetic beads (Life Technologies, CA, USA) and transcribed to cDNA using random oligonucleotides with M-MuLV Rease Transcriptase (RNase H-) (TaKaRa) and DNA polymerase I and RNase H (TaKaRa). NEBNext adaptor oligonucleotides (Illumina) were ligated to the 3' ends of cDNA fragments adenylated with Klenow Exo- (Illumina). Approximate 200 bp cDNA fragments were purified using the AMPure XP bead system (Beckman Coulter, Beverly, USA). Ten cycles of PCR amplifications were conducted to enrich cDNA fragments ligated to the adaptors on both ends using the NEB Universal PCR primer and Index primer (Illumina). The PCR products were purified using the AMPure XP bead system and quantified using the Agilent high sensitivity DNA (Agilent Technologies, CA, USA) on the Agilent 2100 bioanalyzer system. Finally, the four-coded samples were clustered by the cBot cluster generation system using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the user manual, and then sequenced using the 100 bp protocol on an Illumina Hiseq 2000 platform.
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