1. Library preparation – ribosomal RNA depletion method
  2. Illumina Hi-Seq 2000 – 2 x 100bp paired-end sequencing run
  3. Advanced bioinformatics package

Next-Gen DNA Sequencer

LC Sciences provides a transcriptome profiling service using the Illumina high-throughput sequencing technology which enables comprehensive coverage, highly sensitive and specific discovery and profiling of all forms of RNAs in your sample.

This service is comprehensive – from sample to data, providing advanced technology and years of experience in efficient discovery and profiling of RNAs.

Our comprehensive profiling service includes:

  • Sample QC
  • Sample preparation (ribosomal RNA depletion, adapter attachment, reverse transcription)
  • Library preparation (single molecule clonal amplification)
  • High-throughput sequencing (RNA-Seq method, Illumina Next-Gen sequencing technology)
  • Bioinformatics analysis
  • Customer data report

Illumina base-calling and analysis
Raw sequencing data – 100bp paired-end reads – either FASTA-A or FASTA-Q files with base-calling quality scores
LC Sciences quality filtered data reduced to mappable reads, a list of unique sequences and their copy numbers
De novo assembly (if applicable)
Alignment of RNA-Seq reads to customer specified reference genome
Test for differential expression at gene level and transcript level. (biological replicates required – see Technical Note – Biological Replicate Considerations – Differential Expression Analysis)
Identification and construction of splice-junctions
Report of known transcripts with annotation and abundance
Report of novel transcript with abundance
Identification of alternate splicing and report of isoform abundance
GO and KEGG annotation and enrichment analysis

Long non-coding RNA information – map to genome, alignment, annotation and expression info
Optional circular RNA (circRNA) analysis – although the biological function of most circular RNAs is still unclear, some have shown potential as gene regulators
Customer data report – includes a summary of methods and all statistical analysis
Additional Custom Bioinformatics Analysis – If you have additional, more complex bioinformatics needs such as functional gene information mining or comparative genomic analysis, please contact us to learn how we can help get you the results you need to keep your research moving ahead

Sample Data