Arraystar RNA Sequencing profiles mRNAs with excellent coverage. The sequencing library is constructed using dUTP strategy for strand-specific sequencing and unbiased even read distribution along the transcript from 5’ to 3’ end. The paired-end chemistry and long read length allow effective analysis of alternatively spliced transcript isoforms. A comprehensive and easy-to-read mRNA-Seq report is provided along with the complete raw data files.
Degraded RNA sequencing by alternative procedure
mRNA-Seq normally uses oligo(dT) for mRNA enrichment. However, RNAs in many precious sample sources such as FFPE clinical samples may have been partially degraded. The fragmented mRNAs will be lost during standard oligo(dT) enrichment We provide alternative rRNA depletion procedure to remove abundant rRNAs while preserve the mRNA fragments, producing good results even for degraded samples.
The alternative rRNA deletion sample prep should also be used if ncRNA analysis is part of your research interest, as ncRNAs often lack a poly(A) tail.
Please inform us at the initial project consultation if your RNA samples may be partially degraded or ncRNA is to be included in the analysis.
Arraystar has perfected the RNA-Seq technologies, from sample prep, library construction, sequencing and data analysis to obtain upmost sensitivity and accuracy for precise, reliable quantification of differential expression as well as detection of novel transcripts and isoforms.
• Strand-specific and even read distribution
dUTP incorporation in sequencing library construction unambiguously determines sense or antisense RNA transcripts in strand-specific sequencing. The sequencing reads are uniformly and evenly distributed along the entire lengths of the transcripts (Fig. 1)
Figure 1. dUTP RNA-Seq library is highly strand specific and produces unbiased uniform read distribution along the transcript (top track).
• Paired-end Sequencing
Paired-end sequencing allows better assembly, detection, and quantification of RNA transcripts and isoforms as well as discovery of novel ones.
• Splicing Event Detection
Splicing events are identified and novel splice isoforms discovered using junction sequence information with the pair-end reads and deep coverage.
• Comprehensive and easy-to-read analyses
Arraystar mRNA-Seq analyses include QC, mapping, expressional analyses, principal component analysis, correlations, differential expression, clustering, heat maps, gene ontology, pathways, novel gene and transcript discovery, and data visualization.
Comprehensive and easy-to-read analyses are included to help research close to the biology from the RNA-Seq data.
• 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 whether differentially expressed genes occur more often in particular biological functions or pathways.
• RNA-seq data visualization in genome browsers
Advanced Analyses transform the wealth of data into rich information of biology (additional fees apply).
• Gene Set Enrichment Analysis (GSEA) analyzes genes in a functional set that tend to show expressional changes, even if their individual differential expression may not appear strong or significant.
• Regulatory Network Construction for the genes of functional interest.
• High resolution visualization of RNA-seq read distribution along with the exon-intron gene structure, epigenetic modifications, and promoter regions of the gene.
Next-generation sequencing of the basal cell carcinoma miRNome and a description of novel microRNA candidates under neoadjuvant vismodegib therapy: an integrative molecular and surgical case study. Sand M, et al. Ann Oncol, 2016.
Genome-wide Identification of Long Noncoding RNAs in Rat Models of Cardiovascular and Renal Diseases. K Gopalakrishnan, et al. Hypertension, 2014