Next generation sequencing and data analysis
Services do NOT include
Costs for shipment of samples are not included in the service.
Type of analysis to be discussed. For a typical RNA-Seq project: QC of the RNA-Seq sample (un-supervised classification), expression quantification, differential expression analysis, gene set/pathway enrichment analysis. Any final and intermediate data generated during the analysis can be provided including comprehensive, publication ready figures and a protocol of the analytical steps.
Sample Requirements - input of users
If users provide their own total RNA-extracted sample, a mandatory QC and quantification process will be performed in our facilities. On the other hand, if RNA-Extraction with our TECAN robot is requested, input material depends on the RNA/miRNA extraction kit used. Preliminary discussions concerning samples (conservation, storage etc.) are necessary before providing the service.
For direct data analysis, ideally raw data such as compressed fastq files should be provided. It is important to provide us with a descriptive experimental plan (sample bar code, batching information, raw QC data following sequencing) with any available sample preparation quality metrics such as QC of total RNA (RIN numbers) and QC of library preparation (electropherogram profile) to improve data analysis.
Storage of raw data possible on request.
Dr. Adrien Saliou
Description of service
Services include advice on sample selection and experimental design, manual / automated RNA extraction with TECAN robot and quality assessment for RNA sequencing. Bioinformatics / statistics services include data QC, outlier detection and general data management, and data analysis from RNA-Seq (Illumina Technology, NextSeq 500), middle throughput validation system (nCounter nanostring, Biomark fluidigm).
3 weeks, for RNA extraction / QC
4 weeks, for NGS library preparation and sequencing
4 to 8 weeks*, for analysis
Dr. Adrien Saliou
*Strongly depends on analytical goals and quality of the data, Nr of samples and Nr of current projects