NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.
- 1 Announcements
- 2 Data Submission
- 3 Mouse ENCODE Investigators
- 4 Mouse ENCODE Planned Publications
- 5 2011-2012 Consortium Conference Call Documents
- 6 Mouse ENCODE Integrative Analysis
- 7 Analysis Teleconference Schedule and Presentations
- 8 2009-2011 Mouse ENCODE Minutes
- 9 Documents
- 10 Mouse Marker Paper
- 11 Mouse/Human Comparitive Analysis
- 12 Human/Mouse Orthologs
- 13 Protocols
- 14 Mouse Metadata
This page is to organize the groups working on mouse ENCODE projects. 12/14/09
- A listserv has been set up for the Mouse ENCODE group. The listserv address is MOUSEENCODE(at)list.nih.gov. Contact Leslie Adams to be added to this listerv (adamslb(at)mail.nih.gov)
- Recurring mouse ENCODE calls have been scheduled for the third Friday of every month at 1PM ET/10AM PT.
- Remember to update the mouse matrix regularly: https://docs.google.com/spreadsheet/ccc?key=0AvhYvzDpsI4zdGg2SjFHNUtNUUtFMHE1Yjc3WENQblE.
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).
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|
|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
- November 3, 2009
- November 20, 2009
- December 18, 2009
- January 15, 2010
- February 19, 2010; Mike's RNA-seq update
- March 19, 2010
- April 20, 2010
- May 13, 2010
- June 18, 2010
- July 27, 2010
- August 20, 2010
- September 17, 2010
- October 15, 2010
- November 19, 2010
- December 17, 2010
- January 21, 2011
- February 18, 2011
- March 18, 2011
- April 15, 2011
- June 17, 2011
- July 15, 2011
- August 19, 2011
- September 16, 2011
- October 21, 2011
- Proposal for generating mouse ENCODE data for comparison of datasets between labs
- Statement of support for inclusion of David Gifford's work in mouse ENCODE
- Mouse experiments spreadsheet DRAFT as of 11/06/09
- Media:HumanMouse_PeakComparison.ppt Human-Mouse Comparison:Snyder/Hariharan- for 4/20/10 call
- Media:ConservationOfOccupancyTF.ppt Conservation of TF occupancy between mouse and human erythroid cells: Hardison/Cheng - for 5/13/10 call
- Mouse RNA-seq spreadsheet presented by Gingeras lab for 4/15/11 call
Mouse Marker Paper
Mouse/Human Comparitive Analysis
- Human/Mouse Data Comparisons from 1/21/11 call
- Human/Mouse Data Comparisons from 3/18/11 call
- Ren Comparative Analysis Presentation for 7/15/11 call
- Snyder Comparative Analysis Presentation for 7/15/11 call
- Hardison Comparative Analysis Presentation for 8/19/11 call
- Gilbert Comparative Analysis Presentation for 11/29/12 call
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
- JunD-CH12 cells, JunD- MEL cells , JunD-GM12878 cells , JunD-K562 cells- BED files for JunD datasets from Snyder lab for comparison
- All human-mouse orthologs (2012/09/05) ENCODE.human-mouse_orthologs.20120905.txt - MIT+Ensembl protein orthologs & Ensembl ncRNA orthologs
Use this section to post exchange flow protocols, as discussed on the November 3, 2009 mouse ENCODE call.
- Bob Paulson (Penn State) information on stress erythroid progenitors Slides
- Erythroid fractionation slides from Michael Bender
- Mouse B-cell Isolation Protocol from Michael Bender-for 1/21/11 call
Click on the header above for information about registering metadata for ENCODE Mouse experiments.