Genome-wide RNA transcript analysis:
Many biological questions can be addressed by determining the genome-wide patterns of gene expression by measuring RNA levels.
The core facility can provide services including RNA isolation and data analysis, for Ion TorrentTM Proton nextgen sequencing approaches to quantify mRNAs, non-coding RNAs, and small RNAs such as microRNAs. Depending on the method used, we can start with as little as 50 ng of total RNA.
Genome-wide chromatin immunoprecipitation:
Chromatin immunoprecipitation is used to determine where specific proteins bind chromosomes and the locations of histone modifications and other epigenetic marks. These data can provide insights into gene regulatory pathways and epigenetic control of gene expression.
The facility does not prepare chromatin or perform the immunoprecipitation, but can provide suggested protocols and advice for these experiments. Starting from input and precipitated chromatin, the facility can use Ion TorrentTM sequencing to quantify binding or chromatin mark enrichment genome-wide.
Exome and small genome sequencing:
Genetic variations in coding sequences of mammalian and smaller genomes can be discovered by sequencing all known exons and comparing to reference sequences. The Ion TorrentTM also has the capacity to sequence entire small genomes for comparison to a reference genome. We can generate sequences of small genomes for organisms that have not previously been sequenced, but we currently do not provide genome assembly services.
The Ion Torrent ProtonTM sequencing technology is well-suited to sequencing specific sets of genes or other features, such as all known oncogenes, starting with as little as 10 ng of genomic DNA. This feature is useful for re-sequencing of particular gene sets of interest. Life Technologies has many pre-designed amplicon libraries, and custom amplicon libraries can also be designed using web-based tools.
In addition to standard nextgen sequencing services (RNA-seq, ChIP-seq, exome, genome, and amplicon sequencing), custom sequencing protocols can be designed, such as sequencing of selected oligonucleotide libraries. We can also design protocols for measuring nascent RNA and run-on transcription approaches.
Nucleic acid quality analysis:
The core facility uses a QubitTM fluorimeter to quantify small amounts of RNA and DNA. Detailed analysis of size distribution, quantity, and quality is performed using an AgilentTM bioanalyzer. Quality analysis can be provided as a service independent from nextgen sequencing for a nominal cost.
The core facility has installed PartekTM software to facilitate analysis of nextgen sequence data, including gene ontology and pathway analysis. PartekTM provides a graphical user interface that makes it easy for users to conduct their own analysis, but the core facility can also conduct the analysis for users. There is an hourly charge for use of the PartekTM software to cover the cost of the yearly license.
Ion ReporterTM software uses cloud computing to detect genetic variations, such as SNPs, insertions, deletions, and CNVs in genome sequence data.