Svaren Laboratory Project Data

Our laboratory is focused on elucidating molecular events controlling peripheral nerve myelination and this page provides links to supplementary data.

Peripheral Neuropathy Protein Interaction Network

Chromatin Immunoprecipitaton Analysis of Peripheral Nerve Myelination

We have also extended our ChIP analysis of transcription factor binding to locus-wide analysis of Egr2 and Sox10 binding using a custom tiled array of genes that are dynamically regulated in peripheral nerve myelination. These data are published as follows:

Jang, S.W.*, Srinivasan, R.*, Jones, E.A., Sun, G., Keles, S., Krueger, C., Chang, L.W., Nagarajan, R., and Svaren, J. (2010)

Locus-wide identification of EGR2/Krox20 regulatory targets in myelin genes, Journal of Neurochemistry, in press,        *co-first authors, Link to Publication

The raw ChIP-chip data are available from NCBI Gene Expression Omnibus, under accession number GSE23648

Additional supplemental data for this project are listed below as follows:

Supplemental Table S3. Complete list of peaks identified for each factor

Peaks were identified for each replicate of Egr2 and Sox10 ChIP-chip analysis using CMARRT at a false discovery rate of 0.05. For each replicate, the spreadsheet specifies peak chromosome, start, end and overlap with a specific peak from the other replicate using the same antibody. Peak numbers are labeled consecutively on each chromosome.  For Egr2 Ab. 1, 84% of peaks in repeat 1 (445 total) were present in repeat 2 (888 total). For Egr2 Ab. 2, 80.47% of peaks in repeat 1 (640 total) were present in repeat 2 (1877), For Sox10, 60% of peaks in repeat 1 (333) were present in repeat 2 (864). Chromosomal coordinates are derived from RN4 build of the rat genome.

Supplemental Table S4. Overlap Analysis of Egr2 and Sox10 peaks

 For both Egr2 and Sox10 peak analysis, intersection lists were compiled for those peaks that were present in both replicates for Egr2 Ab. 1, Egr2 Ab.2, and Sox10. Chromosomal coordinates are derived from RN4 build of the rat genome.

Supplemental Table S5. Validation assays for selected peaks

Using the specified primers, quantitative PCR assays were performed on independent ChIP samples from P15 rat sciatic nerve using either Egr2 Ab.1 or Egr2 Ab.2. The fold enrichment of Egr2 binding at each site relative to a negative control immunoprecipitation (using rabbit IgG) is indicated.