Project description:Genome editing was conducted on a t(3;8) K562 model to investigate the effects of deleting different modules or CTCF binding sites within the MYC super-enhancer. To check mutations after targeting with CRISPR-Cas9 we performed amplicon sequencing using the Illumina PCR-based custom amplicon sequencing method using the TruSeq Custom Amplicon index kit (Illumina). The first PCR was performed using Q5 polymerase (NEB), the second nested PCR with KAPA HiFi HotStart Ready mix (Roche). Samples were sequenced paired-end (2x 250bp) on a MiSeq (Illumina).
Project description:We have engineered the thermostable KlenTaq DNA polymerase variant called RIV A8 that produces error signatures specific for 5-methylcytosine (5mC) and 5-hydroxycytosine (5hmC) without prior chemical treatment of the DNA samples. These signatures are amplified during DNA amplicon library preparation and are detected by NGS. This method was applied to distinguish C from 5mC and C from 5hmC in DNA templates generated by PCR using modified dCTPs (unmodified by using dCTP, methylated by using d5mCTP, hydroxymethylated by using d5hmCTP).
2024-09-09 | GSE270850 | GEO
Project description:Amplicon-based NGS to detect Cutibacterium acnes phylotypes
Project description:We have engineered thermostable KlenTaq DNA polymerase variants called RIII H20, RIV A8 and RIV D15 that produce error signatures specific for 5-methylcytosine (5mC) without prior chemical treatment of the DNA samples. These signatures are amplified during DNA amplicon library preparation and are detected by NGS. This method was applied to distinguish C from 5mC in DNA templates generated by PCR (unmodified and methylated using the CpG Methyltransferase (M.SssI)). Finally, RIV A8 was used to detect 5mC in HeLa human genomic DNA (native methylation and supplementary methylated using the CpG Methyltransferase (M.SssI))
2024-09-09 | GSE233599 | GEO
Project description:Amplicon NGS to determine staphylococcal species on human skin
| PRJNA702649 | ENA
Project description:Amplicon-based NGS sequencing of CRISPR/Cas9 off-target sites
Project description:We have engineered an RT-active DNA polymerase variant called RT-KTq I614Y that produces error RT‑signatures specific for pseudouridine (Ψ) without prior chemical treatment of the RNA samples. These signatures are amplified during DNA amplicon library preparation and are detected by NGS. This method was applied to distinguish U from Ψ in RNA oligonucleotides (modified or unmodified) used in the previous polymerase screening and oligonucleotides which are designed from the human 18S rRNA at the position around 1445. Finally, RT-KTq I614Y was used to detect Ψ55 in tRNAGly(GCC) from Saccharomyces cerevisiae wildtype compared to data from tRNAGly(GCC) from S. cerevisiae pus4Δ.
