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Oligonucleotide Synthesis

Gene Synthesis & Molecular Biology

Sanger Sequencing

Next Generation Sequencing

Genotyping & Gene Expression

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INVIEW Transcriptome Discover

 

 

Discover and quantify novel transcripts and splicing variants.

INVIEW Transcriptome Discover is a complete RNA-Seq service that provides unique molecular insights into the transcriptome of nearly any organisms. The service can be used to profile all RNA species, including non-coding RNAs. Through the use of strand-specific libraries, the product can also help evaluate both sense and antisense transcripts. The 150 bp paired-end reads can be conveniently used for organisms with longer genes, such as plants. This product is applicable to any sample, as a well-defined reference sequence is not necessary.

 

 

 

 

 

 

 

Applications

 

  • Elucidate cellular function through transcript quantification
  • Analyse specific genomic elements and their biological significance
  • Characterise differences in RNA splicing like alternative splicing
  • Identify antisense transcripts
  • Determine transcribed strand of non-coding RNAs
  • Mark boundaries of closely situated or overlapping genes

Highlights

 

  • Highly sensitive detection of new transcripts or splicing variants
  • Structural information from strand-specific reads
  • Flexible sequencing starting with 30 M guaranteed read pairs
  • Expert BioIT data analysis
  • Comprehensive data report with results presented in different formats
  • Applicable to samples from nearly any organism
  • Availability of reference sequence is not crucial
  • Optional services including RNA isolation and ribosomal RNA (rRNA) depletion

 

 

 

 

 

 

 

Product Specifications & Ordering

 

Starting material

Accepted starting material 

 

  • 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 classification of biological material can be found here (TRBA 466). Please contact us for further information on isolating RNA from material classified as S2.

 

Optional pre-sequencing

  • RNA isolation – efficient isolation of RNA for uniform and less-biased coverage
  • Ribosomal RNA (rRNA) depletion – optimised removal of rRNA from mRNA for commonly studied organisms

 

Please contact us to check the compatibility of your organism

 

Library types

  • Standard eukaryotic library - mRNA is poly-(A) enriched and fragmented. cDNA synthesis is performed using random hexamer priming.
  • Standard prokaryotic library - rRNA is removed by ribo depletion. cDNA synthesis is performed with random hexamer primers.
  • Library with FFPE RNA - RNA isolation from Formalin Fixed Paraffin Embedded (FFPE) samples with optimised ribodepletion for reliable gene expression analysis and SNP detection.
  • Strand-specific library

 

Sequencing specifications

  • Illumina
  • 150 bp paired-end reads
  • 30 million read pairs guaranteed

 

Bioinformatics 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 Ensembl

 

 

Deliverables

  • 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

15 days for up to 192 samples
20 days for up to 400 samples

 

 

 

Literature

 

 

 

 

 

 

 

 

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Quality is important for us

Our products and services are produced and performed under strict quality management and quality assurance systems.

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