Benefits
• Perfected and optimized sample prep, library construction and RNA-seq procedures.
• High efficiency, high quality, cost-effective, unbiased library construction.
• dUTP chemistry to ensure extreme transcript strand-specificity.
• Ultra-high sequencing data quality to maximize the mappable reads.
• Standard analysis package includes advanced in-depth analyses that go beyond the “standard”: Novel gene/transcript discovery, Gene Set Enrichment Analysis (GSEA) for functional prediction, alternative splicing events, and more.

For high integrity intact RNA samples, the service includes poly(A) selection to purify the mRNA in the standard procedure.

For degraded RNA samples, the alternative rRNA depletion procedure to remove the highly abundant rRNAs from sequencing is required separately.

Your samples
Purified total RNA, or Frozen tissues, or cell pellets

Please refer to Sample Submission for details in how to get your project started.

Arraystar RNA-seq
1. Total RNA isolation (Optional) 
2. RNA QC
3. mRNA enrichment by oligo-dT, or separate rRNA depletion for degraded RNA/lncRNA samples
4. Sequencing library construction and library QC
5. Hiseq Sequencer
6. Raw read data processing
7. Data analyses and report
8. Project data delivery

All RNA-seq projects include:
• Raw read data with read quality filtering.
• Adapter trimming.
• Sequencing QC stats.

RNA-seq with Analysis Package includes:
(Available for human, mouse, rat, or species with established genome/transcriptome)
• Expression profiling and differential analysis at gene and transcript levels
• Correlation Matrix, Principal Component Analysis (PCA) and hierarchical clustering heatmaps to visualize sample expression correlation, distances and clusters within and between the groups
• Gene ontology and pathway analyses to explore the differentially expressed genes participating in particular biological functions or pathways.
• Gene Set Enrichment Analysis (GSEA) analyzes the genes in functional sets that tend to show expressional changes, even if their individual differential expression may not appear strong or significant.

Fig 1. GSEA Enrichment Plot of MAPK signaling pathway.

• Alternative Splicing Event Detection identifies and discovers novel splice isoforms using junction sequence information with the pair-end reads and deep coverage. Different types of splicing events such as exon skipping, alternative splice sites and retained introns are detected and profiled for altered RNA processing.

Fig 2. Alternative Splicing events classification.                        Fig 3. Alternative Splicing summary plot.

Patient-derived organoids model treatment response of metastatic gastrointestinal cancers. Vlachogiannis G, et al. Science, 2018

Genome-wide Identification of Long Noncoding RNAs in Rat Models of Cardiovascular and Renal Diseases. K Gopalakrishnan, et al. Hypertension, 2014