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Contents 1 Project Stem Cell to Neuron 2 Plans 3 Individual Project Descriptions 4 Meetings 5 Projects 5.1 iTF (inducible transcription factors) 6 Progress 6.1 Chip-Seq 6.2 Expression Analysis 6.3 ChIP-Chip 6.4 Older Pages 6.5 Software

Project Stem Cell to Neuron

We will build predictive regulatory models of neural development to help us understand what goes wrong in neural pathologies. Using our models we will explore why specific groups of motor neurons die in Spinal Muscular Atrophy (SMA), develop clues for therapeutic targets that might help individuals with SMA, and study how stem cells respond to external cues that could lead to methods of programming stem cells for therapies.

See stemcell.mit.edu for more information.

Background Papers

Plans

16 June 2006 Plans

Project timeline

Talks

Papers under construction

• Hox cluster paper

Individual Project Descriptions

Columbia University
Whitehead Institute for Biomedical Research
Massachusetts Institute of Technology

Meetings

• 16 June 2006 : Columbia University, New York
• 28 September 2006 : Columbia University, New York
• 30 October 2006  : MIT, Cambridge
• 15 February 2007 : Columbia University, New York
• 28 June 2007 : Columbia University, New York
• 24 October 2007  : MIT, Cambridge
• 11 February 2008 : Columbia University, New York

Projects

iTF (inducible transcription factors)

• iTF binding
• iTF cell expression
• Good papers

Progress

Chip-Seq

• Experiment Status
• Analysis
  • ChIP-seq Experiment Summaries
  • ChIP-seq Peaks
  • ChIP-seq Motifs
  • ChIP-seq Peaks vs Expression

Expression Analysis

• Affymetrix Platform
• Initial Tbx20 vs Hb9
• Time Series
  • Quality Control
• Expression and Chromatin Analysis
• iCdx2 Cell Gene-Specific Expression Data
• FISH Experiments
• OliNeu Cell Expression Data
• RA response at Hb9 stage
• SMN1 knockout

ChIP-Chip

• Experimental Platform
  • Antibodies
  • ChIP Protocol Requirements
  • ChipChip Array Design
  • Proposed Initial ChIP-chip Work
  • mES to Olig2-stage Pilot Experiments
  • TF tagging technologies
• Analysis
  • Chromatin Domain Summary
  • Cross-experiment Correlations
  • Analyzing Hb9, Hoxa5, RARgamma factor binding data
  • Positive/negative controls for TF binding
  • Hox-cluster chromatin structure examples
  • Visualizing Hox-cluster chromatin data
  • iCDX2 cell ChIP-chip experiments
• Motif Analysis
  • Known Transcription Factor Motifs
  • Olig2 motif analysis
  • Analyzing H3K4me3/H3K27me3 boundary in the Hox clusters
  • Features associated with chromatin domain boundaries
  • Polycomb Response Elements (PRE)

Older Pages

• Table of Experiments
• Scott's ChIP-chip Analysis Questions
• Gifford Lab Questions and To-Do List

Software

• Hox Viewer
• State Transition Diagrams
• Warpdrive