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De Novo Transcriptome

Identify the genes present in your transcriptome

De novo sequencing of transcriptomes: What is possible?

De novo transcriptome sequencing analyses expressed genes present at a specific time and with a specific physiological background. With the average transcript length of 1,500-2,000 bp, several reads have to be generated per transcript, which are later assembled to reconstruct the full length transcript.

Sequencing our random primed cDNA library on Illumina HiSeq 2500 provides you with tens of millions of 100 bp or 150 bp reads. Usually the output of one channel is way too high for one transcriptome, meaning that several libraries can be analysed in one channel. To your convenience, Eurofins has built up a proprietary software pipeline for de novo assembly of short Illumina reads to cost-efficiently reconstruct the transcripts.

Your advantages:

  • Detect rare or previously unknown transcripts
  • Strand specific protocol (upon request)
  • Cost-efficient de novo transcriptome data

Selected publications about de novo transcriptome sequencing


De novo transcriptome analysis: Højland, D. et al., Adaptation of Musca domestica L. field population to laboratory breeding causes transcriptional alterations. PloS one 9(1)

De novo transcriptome analysis: Merlot, S. et al., The metal transporter PgIREG1 from the hyperaccumulator Psychotria gabriellae is a candidate gene for nickel tolerance and accumulation. Journal of experimental botany

De novo transcriptome with FLX: Safavi-Hemami et al. Diversity of Conotoxin Gene Superfamilies in the Venomous Snail, Conus victoriae. PLoS ONE 9(2)

De novo transcriptome with FLX: Yamauchi et al. Newly Developed SNP-Based Identification Method of Hop Varieties. ASBC 72(4)

De novo transcriptome analysis FLX & gene expression HiSeq: Shimizu et al. Qualitative de novo analysis of full length cDNA and quantitative analysis of gene expression for common marmoset (Callithrix jacchus) transcriptomes using parallel long-read technology and short-read sequencing. PLOS One, 9(6)


De novo transcriptome with FLX: D'Agostino et al. Genomic analysis of the native European Solanum species, S. dulcamara. BMC Genomics 14:356

De novo transcriptome with FLX: Passos M et al. Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycospharella musicola: gene assembly, annotation and marker development. BMC Genomics 14:78


De novo transcriptome with FLX: Urbarova I et al. Digital Marine Bioprospecting: Mining new neurotoxin drug candidates from the transcriptomes of cold-water sea anemones. Marine Drugs 10(10)

De novo transcriptome with HiSeq: Mutasa-Göttgens E et al. A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses. BMC Genomics 13:99

De novo transcriptome with FLX: Hroudova M et al. Diversity, Phylogeny and Expression Patterns of Pou and Six Homeodomain Transcription Factors in Hydrozoan JellyfishCraspedacusta sowerbyi. PLoS ONE 7(4):e36420.


De novo transcriptome with FLX: Windisch H et al. Thermal acclimation in Antartic fish: transcriptomic profiling of metabolic pathways. AJP - Regu Physiol 301, 5

De novo transcriptome with FLX: Kuzina V, et al. Barbarea vulgaris linkage map and quantitative trait loci for saponins, glucosinolates, hairiness and resistance to the herbivore Phyllotreta nemorum. Phytochemistry. 2011 Feb 72, 2-3


De novo transcriptome with FLX: Young, N.D. et al. Elucidating the transcriptome of Fasciola hepatica – A key to fundamental and biotechnological discoveries for a neglected parasite. Biotechnology Advances (2010) 28, 222-231

De novo transcriptome with FLX: Elmer KR. et al. Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times. BMC Biol. 2010 May 12; 8:60

De novo transcriptome with FLX: Johansen SD. et al. Approaching marine bioprospecting in hexacorals by RNA deep sequencing. New Biotechnology, Vol 27


Expression profiling: Torres, T.T., Ottenwälder, B. et al. Gene expression profiling by massively parallel sequencing. Genome Research (2008) 18: 172-177

Bold = Eurofins employee