Transcriptomics involves sequencing all or part of the transcribed RNAs (mRNA, miRNA, non-coding RNAs, etc.) in the genome at a given time and under specific conditions. This technique uses high-throughput sequencing to identify and quantify the transcriptome. These analyses enable the study of gene expression, gene expression networks and alternative splicing mechanisms.
Services
The number of samples to be determined using the PGTB depends on the sequencer, the flow cell and the target number of reads. It is recommended that replicates be included for RNA-seq analyses.
Sequencing can be performed using short reads on the Illumina NextSeq 2000 or using long reads on the Oxford Nanopore Technologies P2 Solo.
Requirements
Illumina sequencing: 1 µg of total RNA and RIN >7
ONT sequencing: Three kits are available, depending on your requirements and the resources available:
- Sequencing of native full-length mRNA strands (>500 ng of mRNA)
- Stranded sequencing of unamplified full-length cDNA (>100 ng mRNA)
- Stranded sequencing of amplified full-length cDNA (>10 ng of mRNA)
Results
Sent by email or uploaded to a server
Depending on the service requested:
- Demultiplexed FASTQ files
- Sequencing run report (MultiQC forIllumina, PycoQC forOxford Nanopore)
- Analyse sur DRAGEN RNA pipeline pour le séquençage Illumina
Associated publications
Lopes, M., Vincent, A., Thomas, F., Clouard, C., Comte, R., Brien, M., Chambeaud, J., Hérault, F., Guichoux, E., Boury, C., Resmond, R., & Merlot, E., 2024. Data paper: Dataset describing the effects of environmental enrichment and sows’ characteristics on the peripheral blood mononuclear cell transcriptome. Animal – Open Space.https://doi.org/10.1016/j.anopes.2024.100078