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This page is to organize the groups working on mouse ENCODE projects. 12/14/09

Data Submission

The most recent status report and experiment spreadsheet are here: 2011-01-21_DCC_Progress#Mouse_ENCODE.

Mouse ENCODE Investigators

  • John Stamatoyannopoulos, Mark Groudine are mapping DNaseI hypersensitive sites and DNaseI footprints using deep sequencing. They will apply these methods to (1) limited mouse cell lines which are analogous to the ENCODE Tier 1 & 2 cell lines in human, and (2) primary mouse tissues from adult animals and embryos, with an emphasis on mouse hematopoietic cells. They are also doing RNA-seq on some cell lines, including ES cells.
  • Mike Snyder and Sherman Weissman are mapping about 30 transcription factors in MEL and CH12 cell lines. Their aim is to compare binding patterns in mouse to those in comparative Tier 1 human cell lines. They propose to map Pol II and three basic histone modifications, as well as do RNA-seq for comparison to human data. Later, they will do the same assays in erythroid precursors.
  • Ross Hardison and collaborators will utilize mouse genetics to enhance human ENCODE by working in knock-out mouse cell lines. They will assay cell lines derived from a GATA-1 knockout derived from ES cell lines, and cell lines where GATA-1 has been restored to force the cells to differentiate to erythroid cells. They will also study a mesodermal line assaying for master regulators of myocytes differentiation. This group will map a handful of factors implicated in differentiation in each of these lineages. They will also work in ES cells and ES differentiated to hematopoietic lineages, as well as some primary cells enriched for BFU-Es and isolated B-lymphocytes. Ross will also bring in Job Dekker as a collaborator to look at chromatin interactions between GATA-1 and MyoD binding sites to responsive genes in their respective cell lines.
  • Bing Ren will identify promoters, enhancers, and insulator elements by studying Pol II, CTCF, two histone modifications and co-activator p300. He will map these elements in 20-30 adult and embryonic tissues as well as ES and MEF cells.
  • Dave Gilbert will provide genome-wide replication timing profiles for several cell types. (Specifically: 3-5 ES and MEF cell lines, MEL, CH12, fetal myoblasts, C127 mammary fibroblasts, L1210 lymphoblasts, CD4+ peripheral T-lymphocytes, 2 EpiSC lines, 3 iPSC lines, as well as ESC-derived differentiation intermediates NPCs, early primitive ectoderm, definitive ectoderm, mesoderm and endoderm).

Mouse ENCODE Planned Publications

2011-2012 Consortium Conference Call Documents

2011 ENCODE Consortium Calls
Date Agenda Scientific Presentation Other Documents Minutes
November 18, 2011 Agenda:111118 Bing Ren November 2011 Minutes
December 16, 2011 Agenda:111216 David Gilbert December 2011 Minutes
January 20, 2012 Agenda:120120 Thomas Gingeras January 2012 Minutes
February 17, 2012 Agenda:120217 Mike Snyder February 2012 Minutes
March 16, 2012 Agenda:120316 John Stamatoyannopoulos March 2012 Minutes
April 20, 2012 Agenda:120420 Ross Hardison April 2012 Minutes
May 18, 2012 Agenda:120518 Bing Ren May 2012 Minutes
June 15, 2012 Agenda:120615 June 2012 Minutes
July 20, 2012 Agenda:120720 July 2012 Minutes
August 17, 2012 Agenda:120817 August 2012 Minutes

Mouse ENCODE Integrative Analysis

Analysis Teleconference Schedule and Presentations

2012 Mouse ENCODE Analysis Calls
Date Agenda Scientific Presentations
July 6, 2012 Agenda:120706 Stamatoyannopoulous/Sandstrom; Feng Yue/Bing Ren; Yong/Richard/Javier/James Taylor
July 12, 2012 Agenda:120712 Yong Chen; Michael Beer
July 19, 2012 Agenda:120719 David Gilbert; Stamatoyannopolous/Sandstrom; Cheng/Snyder
August 2, 2012 Agenda:120802 Bob Thurman/Stamatoyannopoulos;| Giovani Bussotti/Cedric Notredame

2009-2011 Mouse ENCODE Minutes


Mouse Marker Paper

Mouse/Human Comparitive Analysis

Please upload BED files here for data to be tested in the Mouse/Human Comparitive Analysis mapping experiments. Please remember to designate lab affiliation with your upload

Human/Mouse Orthologs

(also available at


Use this section to post exchange flow protocols, as discussed on the November 3, 2009 mouse ENCODE call.

Mouse Metadata

Click on the header above for information about registering metadata for ENCODE Mouse experiments.