Epigenome Profiling – Community Access Opportunity

Sample nomination process

If you would like to nominate samples for consideration, download the sample description form at (CEEHRC Epigenome Profiling Application Form) and submit to info@epigenomes.ca by May 31st, 2018.   If the number of proposed samples exceeds the allocated capacity the CEEHRC executive committee will rank the samples based on tissue and cell types not currently covered within the IHEC reference epigenome collection, purity of the biospecimen and/or perceived ultility to the Canadian epigenetics community.

 

Scope

The CEEHRC Epigenome Mapping Centres located at BC Cancer and UBC and at McGill University are engaged in generating high quality epigenomic datasets and reference maps as part of the International Human Epigenome Consortium (IHEC; ihec.org).

As part of the second phase of the CEEHRC initiative 30% of the funded epigenome mapping capacity has been reserved to profile samples nominated and provided by the Canadian epigenetics research community. As part of the community access program CEEHRC mapping centres will cover the costs of library generation, sequencing and primary data analysis including submission of the resulting sequence and metadata to a public repository from nominated biological specimens that meet requirements described below. 

Epigenomic assays supported by this initiative are listed below, the sum of which constitutes a reference epigenome as defined by IHEC:

  • Histone modifications: Chromatin immunoprecipitation sequencing (ChIP-Seq) using benchmarked antibodies targeting the following histone H3 modifications;
    • H3K4me3
    • H3K4me1
    • H3K9me3
    • H3K27me3
    • H3K27ac
    • H3K36me3
    • input control
  • DNA methylation: whole genome bisulphite sequencing;
  • Transcriptome: Ribodepleted RNA sequencing (RNA-seq)

Processed epigenome datasets will be made available to the submitting groups in the form of raw and processed data tracks.   Browseable ‘tracks’ will also be published within the www.epigenomes.ca and epigenomesportal.ca/ihec data portals and sequence-level data will be deposited at the European Genome-phenome Archive (http://www.ebi.ac.uk/ega/home) as part of the CEEHRC contribution. 

 

Sample Requirements

Biospecimens

  • Samples must be of general interest to multiple research groups. Transgenic / knockout or similarly engineered cell lines designed to investigate research hypotheses will have low priority.
  • Human samples are preferred, but model organism specimens that are relevant to human health and disease will also be considered.
  • Normal and diseased primary cells and primary tissue are preferred, but immortalized cell lines of general research interest are also eligible.
  • Diseased cells/tissue should be accompanied by matched normal equivalents, when possible.
  • Sample sets comprising at least two biological replicates are preferred and should include both male and female representatives when appropriate.

Donor consent and ethical approval

  • Raw sequence datasets derived from this work will be deposited into a protected public repository as per IHEC recommendations and processed tracks will be made publically available to community.  Human subject samples selected for profiling must be approved for this use by the submitting groups institutional Research Ethics Board.
  • Ethics certificates and consent forms must be submitted for review by mapping centre staff prior to sample receipt.

 

Biospecimen Requirements

  • Priority will be given to samples from which a complete reference epigenome (6 histone modifications; WGBS and RNA-seq) can be generated. The minimum requirements for a complete reference epigenome are provided below.   Detailed instructions for sample processing and shipment will be provided prior sample submission by the respective mapping centre.
Requirements – Cells
ChIP-Seq 700k cells minimum; recommend 1M cells
RNA-Seq and WGBS  1M cells as frozen pellet
Back up 1M cells as frozen pellet

 Please contact the mapping centers (GSC-UBC or McGill) for more details and up-to-date information on the minimum requirements.

Requirement - Tissues  
  • Submitters must provide evidence that RNA prep from tissue section yields a RIN > 7
  • Amount of tissue required will be sample dependent but extractions must yield enough nucleic acid to proceed with mapping to proceed. A minimum amount would be 5-10mm cube.     
Purity
  • Sorted primary cells should be at least >80% pure
Metadata

All sample submissions must be accompanied by sample metadata that meet current IHEC requirements (available at http://ihec-epigenomes.org/research/reference-epigenome-standards/