FAQ Genomics/Transcriptomics

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Q. What is the turnaround time of NGS services?

A. The turnaround time depends very much on the technology used and the number of samples submitted. Usually, upon sample delivery, the waiting time until raw data productiuon is 6 to 8 weeks. When users require also for Bioinformatics support, the data analysis may require one or two additional weeks. 

Q. How long do you store customers’ samples?

A. We guarantee sample storage for at least three months after data production. Within this time frame, users are welcome to come pick up their samples at any time.

Q. What is included in your NGS services?

A. Our NGS services always include:

  •  project experiment design and technology feasibility consultation
  •  DNA/RNA quality and quantiity assessment using Agilent Tape Station/Bioanalyzer and Qubit fluorometer 
  •  Library preparation following FGCZ standard protocols 
  •  Library quality and quantiy assessment 
  •  Sequenicing
  •  Sequencing data QC and Demultiplexing 

Q. How many replicates do I need for my RNA-seq experiment?

A. We recommend for all approaches at least 3 replicates. This applies, e.g., when RNA is extracted from cell lines or whole organs, like liver, in sufficient amounts. If one expects considerable variation between replicates because of considerable biological differences (e.g. from human samples) or because the RNA extraction process introduces technical variation (e.g. laser capture micro-dissection) then the number of replicates should be above 5.

Q. How many reads do I need for my RNA-seq experiment?

A. We recommend at least 25 Mio for most eukariotic species. If the RNA-seq should also include pre-spliced and non-coding RNA then the minimum recommendation is 50Mio. If low expressor genes/transcripts are of major concern for the study the numbers should be doubled. 

Q. What read length do I need?

A. We recommend for RNA-seq 75bp or longer. If the focus of the RNA-seq is on splicing effects and aims at isoform assembly and quantification we recommone 125+125bp paired end reads.

 

Q. What data analyses come with my RNA-seq run?

A. The RNA-seq run with bioinformatics includes:

  • base and read qualities (fastqc)
  • contamination check (fastq_screen)
  • alignment statistics (mapping rate, 3’-bias, …)

More analyses can be run on demand. We rely on open source tools for the entire analysis (e.g. tophat or STAR for read alignment, DESeq2, EdgeR for differential expression).

We additionally provide QC reports for:

  • gene and isoform expression estimates for the genome of your choice
  • exploratory data analysis of the expression values
  • differential expression results
  • Gene Ontology analysis

Q. What technologies are available at the FGCZ?

Please refer to our Equipment page and to the links therein for a detailed description of the instruments.

 
Page URL: http://www.fgcz.ch/FAQ/faq-genomics-transcriptomics.html
24.04.2017
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