Regeneromics Shared Resource

DESCRIPTION OF SERVICES AND HOW THEY WILL BE PROVIDED

The RNI Regeneromics Shared Resource will strive to provide cutting edge data analysis through published and novel pipelines.  To not stifle new and emerging techniques and analyses, bioinformatics services will be provided on the per hour or percent effort of project (depending on need) basis after consultation with the RNIRSR.

Key bioinformatic services to be provided from the start are:

  • Microarray and sequencing data analysis. Microarray data should be performed in chip from Affymetrix, Agilent, NimbleGen and Illumina. The sequencing data are including but not limited to RNA-seq, ChIP-seq, ATAC-seq, and scRNA-seq. The analysis will be performed by automated pipeline.
  • Downstream analysis. Downstream analyses are including gene set enrichment analysis, metagene analysis, heatmap plot, motif discovery and customized figure generation such as circus plot, or any accepted figure type from published paper.
  • Data mining from published data. Mining the data downloaded from GEO or the other published database.
  • Consulting for experiment design and analysis. This includes assistance via trouble-shooting for errors received when running the analysis pipeline internally within the affiliated labs.
  • Customized pipeline and tools development. Customized pipeline means to run a pipeline from a given paper and/or to optimize the pipeline to meet the requirements of the affiliated labs experiments.

Prior to onboarding projects, consultation with the Bioinformatician will occur at no cost.  During consultation, the lab will be able to engage with the Bioinformatician about analyses to be performed and expected deliverables.  After consultation, the Bioinformatician will provide an estimate of the cost of completion, as well as an average expected date of completion.  At this time, the project will be lined up in the queue with a 48 hour hold for the lab to agree to the terms of the analysis.  Should a lab take longer than 48 hours to agree to the terms, they will be removed from the queue and the expected date of completion will be reassessed upon receipt of the agreement.  Should the lab request new and/or additional analysis after the start or completion of the project, the Bioinformatician will determine a new expected cost of completion and timeline for completion.

We will collaborate with CoreResearch@Duke to provide billing support.  To this end, a lab will agree to the terms of analysis by accessing the RNIRSR through CoreResearch@Duke and provide the billing information.

The RNIRSR will ask affiliated labs using the services to list the RNIRSR in the acknowledgements of any publications unless authorship is warranted based on effort.  This will be discussed during initial consultations and will be reassessed if needed.  RNI affiliated labs will be asked to list their affiliation on publications when using the RNIRSR.

Please email rnirsr@duke.edu for consultation or further information.