What Information Do You Require About My Project?

Consultations

We can provide better advice on appropriate or optimal sequencing options if you provide us important background information on your project. We suggest using the questions below as a starting point for inquiries.

Information requested for RNA-sequencing projects:

  • Which species are you studying (prokaryotic or eukaryotic)?
  • From which sample types will the RNA be isolated (e.g. tissues, cell cultures, whole organisms)?
  • What is the objective of the study (e.g. differential gene-expression (DGE) study, gene annotation, identification of iso-forms)?
  • For differential DGE studies: Are you interested only in gene-level DGE, or do you want to study the expression of the different transcripts of genes? Are you interested in non-coding RNAs?
  • Do you expect lowly expressed genes to become important for your study?
  • How closely are related (genetically) are the biological replicates?
  • Do you expect to induce strong phenotypic changes by the varying treatments?
  • What total RNA amounts do you expect to extract from the samples?
  • What is the expected integrity of the RNA samples (e.g. RIN-scores)? Do you expect potentially interfering chemicals in the samples (e.g. phytochemicals)?
  • How many samples do you want to study? Will the samples be available at the same time?

RNA-seq options are described on two pages: RNA-seq and 3′ Tag-Seq Gene Expression Profiling.

Information requested for DNA-sequencing projects:

  • Which species are you studying (prokaryotic or eukaryotic)?
  • What type of samples are you going to submit (e.g. genomic DNA, amplicons, metagenomic samples, purified strain or population samples)?
  • What is the expected genome size? What genome coverage are you aiming for?
  • What is the objective of the study (e.g. SNV variant analysis, genotyping, de novo genome assembly, structural genome variants, metagenomic analysis)?
  • For de novo genome assemblies: Are you interested in genic regions or do you require the full genome sequence? Do you require the ordering of the assembly scaffolds?
  • What DNA amounts do you expect to extract from the samples?
  • What is the expected DNA sample integrity (fragment sizes)? Do you expect potentially interfering chemicals in the samples (e.g. phytochemicals)? What protocol are you using for the DNA isolation?
  • How many samples do you want to study?

Most DNA-Seq options are described here.

 In-Progress Project Inquiries

To be able to help you quickly with current or recent projects we always need the following information:

  • PI name
  • Submitter name
  • Project ID  (e.g.  HiSeq3421)
  • Submission date (even if vague)

 


Category: 01 General Information

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