INVIEW Transcriptome Explore

Overview
Product Details

INVIEW Transcriptome Explore

Reliable transcript identification and comparison between expression levels

INVIEW Transcriptome Explore is an attractive sample-to-result package that provides general characterization of a specific transcriptome using RNA-Seq. The product enables the comparative analysis of genes expressed at a given time or under specific conditions. The raw data is carefully analyzed by trained bioinformaticians to produce a clear and informative report of all sequencing results.

Applications

Comparison studies of highly expressed genes
Analysis of transcript levels from different samples
Screening approaches where reference sequences are available
Gene expression profiling in cancer

Highlights of INVIEW Transcriptome Explore

Strand-specific cDNA libraries for sequencing with Illumina's technology
30 million single reads guaranteed
Ideal for screening projects with high sample throughput
Well suited to comparison studies of gene expression

Product specifications

Processing of any number of samples, starting with one sample
Preparation of random primed cDNA libraries
RNA-Seq with leading sequencing technology
Adaptable sequencing output in multiples of 30M reads
High-quality BioIT analysis
Final report with ready-to-publish data
Available under ISO 17025 accreditation
Requires a well-known reference genome/transcriptome

INVIEW Transcriptome Explore offers a powerful method for profiling and comparing transcripts in order to explore gene structure and function. The NGS-based approach offers general transcriptome analysis using RNA-Seq. The transcriptome-sequencing service extracts valuable information from carefully prepared random primed cDNA libraries. Following thorough BioIT analysis (Fig. 1), a comprehensive report of all results can be delivered in rapid turnaround times.

Fig. 1 BioIT analysis involved in the determination of gene expression levels

For projects without a reference genome, de novo transcriptome sequencing based on PacBio technology can be added to your project. See section below on "Related Products".

Learn more about the INVIEW Transcriptome Explore package

Starting Material

Accepted starting material for INVIEW Transcriptome Explore

Total RNA from various sources
rRNA-depleted total RNA

Accepted starting material for RNA isolation

Tissue
Cells
Body fluids
FFPE tissue

Please note that only S1-classified material is accepted for RNA isolation ordered online. More information about the current rules for classifying biological material can be found here. Please contact us for further information on isolating RNA from material classified as S2.

Specifications

Library types

Standard eukaryotic library - mRNA is poly-(A) enriched and subsequently fragmented. cDNA synthesis is performed with random hexamer priming.
Standard prokaryotic library - ribosomal RNA is removed by ribo depletion. Random hexamer primers are used for cDNA synthesis.
Library with FFPE RNA - RNA isolation from Formalin-Fixed Paraffin Embedded (FFPE) samples. An optimised workflow including ribodepletion allows for reliable gene expression analysis and SNP detection.

Sequencing platform

Illumina

Sequencing mode

50 bp single reads
30 million single reads guaranteed

Bioinformatics offered for transcriptome analysis

Semi-automatic mapping against one reference
Identification of potential exon-exon splice junctions
Identification and quantification of transcripts
Merging of identified pieces to full-length transcripts
Transcript annotation based on known annotations
Determination of expression levels
Pairwise comparison of expression levels and determination of significant fold differences
Detection and annotation of SNPs and InDels
Annotation of detected SNPs and InDels that are registered in dbSNP
Allocation of protein-level effects that are registered in Ensemble

Deliverables of bioinformatic analysis

Alignment file (BAM)
Gene expression table including FPKM value (tsv)
Combined gene expression table of all samples (tsv)
Table of top genes expressed (tsv)
Table of pairwise differential gene expression including foldchange and p-value (tsv)
Table of genes expressed differently between pairs (tsv)
SNP and InDel tables including annotated variants and effects (vcf, tsv, bed)
Comprehensive Data Analysis Report (.pdf)

Delivery time