Laboratory Methods

The Epigenomics program has transitioned from Common Fund support. For more information, please visit https://commonfund.nih.gov/epigenomics.

Please note that since the Epigenomics program is no longer supported by the Common Fund, the program website is being maintained as an archive and will not be updated on a regular basis.

The Common Fund supported Epigenomics program produced reference epigenomes of a wide-range of normal cell types that can be used by the community for a variety of purposes. This was made possible through the development of protocols that leveraged advancements in next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility, and small RNA transcripts in stem cells and primary ex vivo tissues. The Roadmap Epigenomics Consortium (link is external) also made these protocols as well as data standards available and they can be downloaded here.

Experimental Protocols

Methylome Analysis

• 5xMRE-Seq Library Construction Protocol V5
  June 15, 2011 — November 2010 -- Costello Lab
• MeDIP-Seq Library Construction Protocol V2
  June 15, 2011 — June 2010 -- Costello Lab
• MethylC-Seq Library Preparation Protocol
  April 19, 2010 — Ecker Lab
• Preparation of Reduced Representation Bisulfite Sequencing Libraries for Genome-Scale DNA Methylation Profiling
  March 18, 2011 — Broad Institute
• Triple-MRE-Seq Library Construction Protocol V5
  June 15, 2011 — March 2011 -- Costello Lab

DNase1

• Human Hematopoietic Cells: DNase1 Treatment, Crosslinking, and Preserving Cells for RNA
  Feb. 10, 2011 — UW Stam Lab
• Nuclei Isolation from Human Tissue Using a Dounce Homogenizer
  Feb. 10, 2011 — UW Stam Lab
• Nuclei Isolation from Human Tissue Using GentleMACS Dissociator
  Feb. 10, 2011 — UW Stam Lab

General Protocols

• Lymphoid Cells from Apheresis, Freezing
  Feb. 10, 2011 — UW Stam Lab
• Lymphoid Cells from Apheresis, Slow Thawing
  Feb. 10, 2011 — UW Stam Lab
• SLX-PET Protocol for Illumina Sample Prep (link is external)
  April 19, 2010 — BC
• Small Amount DNA Solexa Library Construction – Aug 2009
  April 19, 2010 — Broad
• Solexa Indexed Paired-End Library Construction
  Feb. 10, 2011 — UW Stam Lab
• Solexa Paired-End Library Construction
  Feb. 10, 2011 — UW Stam Lab

ChIP-Seq

• ChIP Protocol for Full REMC (6 Marks)
  April 19, 2010 — Broad
• Isolation of Modified Histones from Chromatin
  April 19, 2010 — Ren Lab
• Peptide Dot Blot Antibody Specificity Screening
  April 19, 2010 — Ren Lab
• Prepare ChIP-Seq DNA Library for Solexa
  April 19, 2010 — Ren Lab
• REMC ChIP and Library Construction Protocol
  Jan. 31, 2011 — Farnham Lab

RNA Analysis

• SLX Transcriptome Library Construction Day 1 (link is external)
  April 19, 2010 — BC
• SLX Transcriptome Library Construction Day 2 (link is external)
  April 19, 2010 — BC
• SLX-Micro RNA2 (link is external)
  April 19, 2010 — BC
• Total RNA Extraction from Cells UW-NREMC
  Feb. 10, 2011 — UW Stam Lab
• Total RNA Extraction from Tissues UW-NREMC
  Feb. 10, 2011 — UW Stam Lab

Data Standards

Methylome Analysis

• Standards and Guidelines for Whole Genome Shotgun Bisulfite Sequencing
  Dec. 2, 2011 —

ChIP-Seq

• REMC Standards and Guidelines for ChIP-Seq
  Dec. 2, 2011 — V1.0

RNA Analysis

• REMC Standards and Guidelines for RNA-Sequencing
  Dec. 2, 2011 — Draft V3.0