Services
AGRFs Next-Generation Sequencing services are based on long and short tag sequencing technologies. The GS FLX generates longer read lengths for applications including de novo genome sequencing and re-sequencing. Applications that use short reads, but require greater sequencing depth at a lower cost include ChIP-Seq which can be performed on the GA II.
This service allows for a variety of different projects for a range of high throughput sequencing applications, including, but not limited to:
AGRF utilises the Roche GS FLX and illumina GA II platforms for the next-generation sequencing service. Please refer to the service process for each platform as per below.
illumina GA II Service Process
Roche GS FLX Service Process
RNA Sequencing
Transcriptome sequencing is a term that encompasses many applications including:
- mRNA transcript-expression analysis (full-length mRNA, expressed sequence tags (ESTs) and ditags)
- Novel gene discovery
- Gene space identification in novel genomes
- Assembly of full-length genes
- Single-nucleotide polymorphism (SNP)
- Insertion - deletion and splice-variant discovery as well as analyses of allele-specific expression and chromosomal rearrangement
ChIP-Seq
ChIP-Seq is used to analyze protein interactions with DNA by combining chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing. ChIP-Seq enables precise analysis of the binding sites of transcription factors, replication and transcriptional machinery, structural proteins such as histones, as well as the impact of protein modifications on genome occupancy.
De Novo Sequencing
By utilising long shotgun and large insert paired end reads, contiguous sequence information covering highly repetitive regions of complex genomes can be obtained and assembled.
Paired End Sequencing
This application is ideal for aligning contigs generated from the whole genome shotgun approach enabling genome closure to proceed more rapidly. Besides helping with de novo assemblies, paired reads can help to detect structural variations in the genome like insertions or deletions, copy number variations, and genome rearrangements.
Deep Sequencing
Amplicon Sequencing allows “Ultra Deep Sequencing” of one or multiple target sequences of interest, allowing the process of detection, identification and quantification of low-level (≥5%) DNA variants in a population. Typical applications of Amplicon re-sequencing include the investigation of:
- Correlations between specific mutations and disease
- Diversity in clinical samples
- Diversity in environmental samples
- Population studies to find rare alleles
Metagenomics
By utilising next-generation sequencing technologies, microorganism communities can be studied in their natural environments thus eliminating the need to culture these organisms. These techniques are particularly useful for those organisms which are difficult to culture.
