Roadmap Epigenome Project Protocols Database
Data Standards
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REMC Standards and Guidelines for ChIP-seq
v1.0
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REMC Standards and Guidelines for RNA-sequencing
DRAFT v3.0
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Standards and Guidelines for Whole Genome Shotgun Bisulfite Sequencing
Experimental Protocols
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5xMRE-seq library construction protocol v5
November 2010 -- Costello Lab
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ChIP Protocol for Full REMC (6 marks)
Broad
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Human hematopoietic cells: DNaseI treatment, crosslinking, and preserving cells for RNA
UW Stam Lab
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Isolation of modified histones from chromatin
Ren Lab
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Lymphoid cells from apheresis, Freezing
UW Stam Lab
Experimental Protocols
Methylome Analysis
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5xMRE-seq library construction protocol v5
June 15, 2011 — November 2010 -- Costello Lab
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MeDIP-seq library construction protocol v2
June 15, 2011 — June 2010 -- Costello Lab
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MethylC-seq library preparation protocol
April 19, 2010 — Ecker Lab
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Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
March 18, 2011 — Broad Institute
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Triple-MRE-seq library construction protocol v5
June 15, 2011 — March 2011 -- Costello Lab
DNaseI
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Human hematopoietic cells: DNaseI treatment, crosslinking, and preserving cells for RNA
Feb. 10, 2011 — UW Stam Lab
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Nuclei isolation from human tissue using a Dounce homogenizer
Feb. 10, 2011 — UW Stam Lab
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Nuclei isolation from human tissue using gentleMACS Dissociator
Feb. 10, 2011 — UW Stam Lab
General Protocols
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Lymphoid cells from apheresis, Freezing
Feb. 10, 2011 — UW Stam Lab
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Lymphoid cells from apheresis, Slow Thawing
Feb. 10, 2011 — UW Stam Lab
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SLX-PET Protocol for Illumina Sample Prep
April 19, 2010 — BC
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Small Amount DNA Solexa Library Construction – Aug 2009
April 19, 2010 — Broad
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Solexa Indexed Paired-End Library Construction
Feb. 10, 2011 — UW Stam Lab
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Solexa Paired-End Library Construction
Feb. 10, 2011 — UW Stam Lab
ChIP-Seq
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ChIP Protocol for Full REMC (6 marks)
April 19, 2010 — Broad
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Isolation of modified histones from chromatin
April 19, 2010 — Ren Lab
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Peptide Dot Blot Antibody Specificity Screening
April 19, 2010 — Ren Lab
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PrepareChi-Seq DNA Library for Solexa
April 19, 2010 — Ren Lab
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REMC ChIP and Library Construction Protocol
Jan. 31, 2011 — Farnham Lab
RNA Analysis
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SLX Transcriptome Library Construction Day 1
April 19, 2010 — BC
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SLX Transcriptome Library Construction Day 2
April 19, 2010 — BC
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SLX-micro RNA2
April 19, 2010 — BC
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Total RNA Extraction from Cells UW-NREMC
Feb. 10, 2011 — UW Stam Lab
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Total RNA Extraction from Tissues UW-NREMC
Feb. 10, 2011 — UW Stam Lab
