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. Sequencing by illumina platform
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.

• Cellular sources of IL-6 and associations with clinical phenotypes and outcomes in PAH. Simpson C E, et al. European Respiratory Journal, 2020
• Ins****-like growth factor binding protein-2: a new circulating indicator of pulmonary arterial hypertension severity and survival. Yang J, et al. BMC medicine, 2020
• The Role of Crosstalk between AR3 and E2F1 in Drug Resistance in Prostate Cancer Cells. Xu J, et al. Cells, 2020
• RNA-seq Analysis of Wild-Type vs. FOXC2-Deficient Melanoma Cells Reveals a Role for the FOXC2 Transcription Factor in the Regulation of Multiple Oncogenic Pathways. Hargadon K M, et al. Frontiers in Oncology, 2020
• Fermentable Fibers Induce Rapid Macro and Micronutrient Depletion in Toll-like Receptor 5 Deficient Mice. Golonka R M, et al. American Journal of Physiology-Gastrointestinal and Liver Physiology, 2020
• Fermentable fiber-induced hepatocellular carcinoma in mice recapitulates gene signatures found in human liver cancer. Chandrashekar D S, et al. PloS one, 2020
• Profiling the microRNA signature of the peripheral sensory ganglia in experimental autoimmune encephalomyelitis (EAE). Friedman T N, et al. Journal of neuroinflammation, 2019
• MYC deregulates TET1 and TET2 expression to control global DNA (hydroxy) methylation and gene expression to maintain a neoplastic phenotype in T-ALL. Poole C J, et al. Epigenetics & chromatin, 2019 
• The FOXC2 Transcription Factor Promotes Melanoma Outgrowth and Regulates Expression of Genes Associated With Drug Resistance and Inter***** Responsiveness. HARGADON K M, et al. Cancer Genomics-Proteomics, 2019
• Complexity of the microRNA transcriptome of cow milk and milk-derived extracellular vesicles isolated via differential ultracentrifugation. Benmoussa A, et al. Journal of dairy science, 2019
• Subendothelial stiffness alters endothelial cell traction force generation while exerting a minimal effect on the transcriptome. Bastounis E E, et al. Scientific Reports, 2019
• Patient-derived organoids model treatment response of metastatic gastrointestinal cancers. Vlachogiannis G, et al. Science, 2018
• MYC deregulates TET1 and TET2 expression to control global DNA (hydroxy) methylation and gene expression to maintain a neoplastic phenotype in T-ALL. Poole C J, et al. Epigenetics & chromatin, 2019
• Subendothelial stiffness alters endothelial cell traction force generation while exerting a minimal effect on the transcriptome. Bastounis E E, et al. Scientific Reports, 2019
• Impairment of Fatty Acid Oxidation in Alveolar Epithelial Cells Mediates Acute Lung Injury. Cui H, et al. American journal of respiratory cell and molecular biology, 2019
• The FOXC2 Transcription Factor Promotes Melanoma Outgrowth and Regulates Expression of Genes Associated With Drug Resistance and Inter***** Responsiveness. HARGADON K M, et al. Cancer Genomics-Proteomics, 2019
• Complexity of the microRNA transcriptome of cow milk and milk-derived extracellular vesicles isolated via differential ultracentrifugation. Benmoussa A, et al. Journal of dairy science, 2019
• Genome-Wide Identification of Long Noncoding RNAs in Rat Models of Cardiovascular and Renal Disease. K Gopalakrishnan,et al. Hypertension, 2014