RNA sequencing (RNA-Seq) is a highly sensitive and accurate tool for measuring gene expression across the transcriptome, allowing the detection of changes occurring in disease states, in response to therapeutics, under different environmental conditions, and across a broad range of other study designs. RNA-Seq allows researchers to detect both known and novel features in a single assay, enabling the detection of transcript isoforms, gene fusions, single nucleotide variants, and other features without the limitation of prior knowledge.
Our standard service includes alignment of short reads to an appropriate genome, data quality control and normalization, identification of differentially expressed genes between sample conditions, and functional gene enrichment analysis (KEGG and Gene Ontology).
- Quality control of raw sequencing reads
- Alignment to standard reference genome and mapping to appropriate gene annotations
- Gene-level abundance measurements
- Data normalization (read depth and transcript length)
- Sample-to-sample quality assessment via unsupervised hierarchical clustering and principal component analysis
- Determination of sample outliers and/or batch effects, and recommendations for downstream analysis
- Differential expression testing for sample pairs (condition A vs condition B)
- Functional gene enrichment analysis (GO, KEGG)
Extended services are available, which supplement our standard/fixed workflow described above:
- Acquiring data from 3rd party services, such as ArrayExpress or GEO
- Depositing data to public repositories, such as ArrayExpress or GEO
- Iterative customization of results and plots for presentations, publications, grants, etc...
- Batch correction and modeling
- Gene-Set Enrichment Analysis (GSEA)
- Integration with other data