Available Services
In this section, you may browse through all services available across all National Facilities. Use the filter function to filter services by National Facility, Infrastructural Unit or category of service. In addition, you may use the text search function to search across services using key words. Please note the system will search your chosen key word either in the service title or description.
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Nanopore small gDNA sequencing (long reads)
The native barcoding kit enhances nanopore sequencing by enabling simultaneous sequencing of multiple samples with unique barcodes. After gDNA extraction, each sample is tagged with a barcode during library preparation. Sequencing generates long reads, allowing real-time base calling. Bioinformatics tools can be used to analyze data, including aligning reads and variant calling. This approach is particularly useful for studying small bacteria genomes because it is cost-effective and efficient, beneficial for microbiome studies and environmental monitoring and other applications in microbial genomics.
Libraries are prepared with the Native Barcoding Kit 96 V14 that enables PCR-free multiplexing of small gDNA samples using 96 unique barcodes. It involves repairing and dA-tailing gDNA, then ligating a unique dT-tailed barcode adapter. Barcoded samples are pooled, and each barcode adapter ligates to a sequencing adapter. Optimized for high sequencing accuracies (>99% Q20+) on nanopore Flowcells R10.4.1.
Nanopore gDNA sequencing (long reads or ultra long reads)
Nanopore sequencing directly sequences DNA using nanopores, known for producing long or ultra-long reads. Protocol includes DNA extraction, minimal fragmentation for long reads or no fragmentation for ultra-long reads generation, DNA end repair, adapter ligation, device setup, sequencing, and data collection through electrical signals. Base-calling converts signals into DNA sequence. Data analysis involves error correction, read filtering, and read assembly.
The library prep method for long-read sequencing involves repairing DNA ends, dA-tailing, and ligating sequencing adapters. It achieves >99% sequencing accuracy (Q20+) on R10.4.1 flow cells. It is compatible with target enrichment, whole genome amplification, and size selection.
The Ultra-Long DNA Sequencing library prep method facilitates preparation of ultra-high molecular weight DNA, yielding N50s >50 kb and reads up to 4+ Mb. Utilizing transposase chemistry, it cleaves template molecules and attaches tags, followed by rapid adapter addition.
Nanopore Direct RNA Sequencing
Direct RNA Sequencing with Nanopore technology sequences RNA molecules without cDNA conversion, offering real-time detection of RNA sequences and modifications. It preserves RNA’s native state, revealing insights into RNA processing and modifications. RNA extraction, adapter ligation, sequencing, and data analysis are key steps. Raw signals are base-called for RNA sequence reconstruction. This method can offer a comprehensive view of the transcriptome.
The Direct RNA Sequencing Kit (SQK-RNA004) facilitates native RNA sequencing, avoiding cDNA conversion. It supports poly(A)-tailed RNA or total RNA like eukaryotic mRNA and viral RNA. This upgrade enhances sequencing output and accuracy on the latest RNA flow cells (FLO-MIN004RA and FLO-PRO004RA). It includes reformulated priming reagents for flow cell compatibility and features fuel fix technology for extended experiment runs without additional fuel.
Nanopore cell-free DNA sequencing (Human)
Cell-free DNA (cfDNA) sequencing with Nanopore technology allows direct interrogation of genetic information in circulating DNA without PCR amplification. This real-time protocol enables methylation status analysis. It offers insights into cfDNA’s genomic landscape, benefiting clinical diagnostics like cancer detection, treatment monitoring, and minimal residual disease identification. The protocol involves cfDNA extraction, library preparation, loading onto a Nanopore sequencing device, real-time sequencing, and data analysis for variant calling, copy number and methylation status analysis.
The library preparation involves repairing DNA ends, dA-tailing, and ligating sequencing adapters. The kit ensures high sequencing accuracies (Q20+) on nanopore Flowcells R10.4.1, with updates for enhanced DNA capture and fuel fix technology for longer runs. The protocol is optimized for short DNA fragments recovery, based on a modified long-reads protocol.
Nanopore cDNA sequencing (bulk cDNA or single-cell cDNA from 10x Genomics protocol) (Human-Mouse)
Nanopore cDNA sequencing allows the exploration of gene expression dynamics, alternative splicing, and RNA biology with long-read capabilities. The process involves RNA extraction, cDNA synthesis, library preparation with unique barcodes, loading onto a nanopore sequencer, real-time sequencing of cDNA strands, base calling, and subsequent bioinformatics analysis for aligning reads, identifying gene isoforms, and quantifying gene expression.
The libraries are prepared with the PCR-cDNA Sequencing Kit that enables nanopore sequencing of cDNA from low input poly(A)+ RNA or total RNA with additional optimization. It employs a strand-switching method to select full-length transcripts and incorporates unique molecular identifiers (UMIs). The kit includes the Rapid Adapter T (RAP T) for enhanced capture and fuel fix technology for longer experiments without fuel addition. A new cDNA RT adapter and RT primer reduce overlaps during reverse transcription and allow measurement of polyA+ tail lengths.