omiics | Total/long RNA

TOTAL RNA SEQUENCING

Sub-categories:

Total RNA-seq, transcriptome analysis, mRNA-seq, Long non-coding RNA-seq, RNA-seq for quantification & 3’end sequencing

Characterizing transcriptome dynamics by sequencing

While the genome in an organism is considered to be mostly static over time, changes associated with development, aging and disease is reflected in the transcriptome. Comparative studies applying RNA-seq enables investigation of changes in expression level, isoform usage and regulatory events as circularization.

While each project is unique and consequently the optimal solution varies according to the settings, some elements will be fairly consistent across most experiements.

A complete omiics standard project for small RNA sequencing include:

Long RNAs

mRNA

lncRNA

circRNA

The project starts with a meeting with a NGS-scientist, where your research

and material is discussed and the optimal startegy is designed.

LABORATORY

RNA extraction
Whole transcriptome enrichment by rRNA depletion*
Library preparation

- 250-300 bp insert cDNA library
- Multiple kit options available

Stranded sequencing**

* PolyA-enrichment or cDNA capture is also available, however, we highly recommend using rRNA removal as this provides data on both coding and noncoding RNAs.

** Non-stranded sequencing is available, however, gives you less valuable data and while historical cheaper, the current prices are identical.

SEQUENCING

Platforms: HiSeq4000, HiSeq3000 or NextSeq500
≥50 Million reads/sample (≥25 Million reads for 3’end-seq)
100bp or 150bp PE sequencing (50bp/75bp SE for 3’end-seq)

PE: Paired-end, SE: Single-end

BIOINFORMATICS

Quality control - scoring of reads and adaptor removal (assessment of sequencing statistics)
Mapping to known genome/transcriptome (alignment) or De novo assembly (including sequencing assessment/alignment statistics)
Differential expression analysis and cluster analysis (Gene expression annotation, expression pattern analysis, Hierarchical clustering analysis, PCA analysis, quantitative expression profiles)

REPORT AND DISCUSSION

Tables (.excl*)
Publication-grade figures (.TIFF*)
Written report summarizing the procedure and results done by omiics
Follow-up meeting with PhD-level NGS-scientist from omiics discussing results, suggestions for interpretation and input on possible next step(s)

* Other formats are also available if requested

More info on input material

Additional

options

below

or Species?

Additional Bioinformatic Analysis for Total RNA sequencing

Pathway analysis (Gene ontology analysis, Pathway enrichment analysis
Network analysis, including Condition specific expressed analysis, Gene Co-expression Network
Analysis, Time series analysis
CircRNA detection and circRNA differential expression analysis
Alternative splicing/isoform usage analysis/Fusion gene analysis
LncRNA detection and function prediction /LncRNA Family prediction and classification
SNP and Indel detection
Protein-Protein Interaction (PPI) analysis
Comparison with online available data (Data-mining)

Customized analysis - contact us to discuss your needs