Full transcriptomic analyses

Identification and quantification of expressed genes

Your transcriptome project

Transcriptomic differences between organisms, developmental stages and environmental conditions can be comprehensively compared through RNA sequencing. The determination of transcript abundance (gene expression profiling) and annotation of coding SNPs is a powerful tool to study underlying mechanisms that lead to specific phenotypes. Due to its high reproducibility and wide dynamic range RNA sequencing can be applied in many medical and biological research fields.

Strategy

To reliably determine the relative abundance of transcripts and compare expression levels from different samples ultra deep sequencing has to be performed. The Illumina HiSeq 2000 provides the industry's highest sequencing output and quality at fastest data generation rate and can be optimally used to perform a deep investigation of the transcriptome. The sequencing of full-length cDNA allows to study polymorphisms in the coding part of the transcripts and to simultaneously quantitatively measure their abundance. Focused studies on the hyper-polymorphic and information-rich 5’ or 3’ untranslated regions (UTRs) can be performed through preparation of specific libraries. The use of 5’- or 3’-UTR libraries also increases the depth of sequencing and hence the change to detect low abundant but physiologically relevant transcripts.

Starting material

• tissue
• total RNA
• mRNA
• cDNA

Library preparation

• Optional: mRNA enrichment / rRNA depletion for prokaryotes
• Random primed cDNA synthesis for full length cDNA sequencing
• 3’- or 5’-UTR libraries to specifically focus on the information-rich untranslated regions and to increase the depth of sequencing

Sequencing

• Illumina HiSeq 2000 | single or paired end reads for SNP discovery and expression analyses

Bioinfomatic

• Raw data (fastq)
• Clustering
  • Representative of each cluster (fasta)
  • Clustering table (tsv)
• Alignment
  • Alignment file (sam, bam)
  • Expression profile table (tsv)
  • Number of hits to same transcript (txt)
  • Table of all SNPs (tsv)
• Sample comparison
  • Comparative table (tsv)
  • Scatter plot (pdf)

• Pre-Sequencing
• Single Reads
• Genomes
• Targeted (re)-sequencing
• Human Sample Sequencing
• Transcriptomes
  • > De novo Sequencing
  • > Re-Sequencing
• Metagenome
• Regulome

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