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BioMed Research International
Volume 2015, Article ID 202914, 13 pages
Research Article

Epigenomics of Neural Cells: REST-Induced Down- and Upregulation of Gene Expression in a Two-Clone PC12 Cell Model

1Scientific Institute San Raffaele, Center for Translational Genomics and Bioinformatics, 20132 Milan, Italy
2CNR Institute of Neuroscience, 20129 Milan, Italy
3Humanitas Research Center, Rozzano, 20089 Milan, Italy
4Boehringer Ingelheim, 88400 Biberach an der Riß, Germany
5Division of Neurosciences, San Raffaele Institute and Vita-Salute San Raffaele University, 20133 Milan, Italy

Received 16 March 2015; Accepted 16 July 2015

Academic Editor: Salvatore Spicuglia

Copyright © 2015 Jose M. Garcia-Manteiga et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

Short description of Supplementary Materials The supplementary materials report details about the potential REST target genes revealed by RNA-Seq (Si Table 1) and about the Enrichment Analyses of various, specific populations of potential target genes, down- and upregulated in hrREST cells. Specifically, Si Tables 2 and 3 report about ENCODE TF and ChAE genes down- and upregulated; Si Tables 4 and 5 about the pathway enrichment of the same genes; Si Table 6 about TF protein-protein interactions.

Table S1. Differential Expression Analysis by DESEq of hrPC12 down-regulated (log2 Fold change <2) and up-regulated (log2 Fold change >2) genes.

Table S2. ENCODE Transcription Factor (TF) and ChEA database ChIP-seq Enrichment Analysis of down-regulated genes in hrPC12 cells.

Table S3. ENCODE Transcription Factor (TF) and ChEA database ChIP-seq Enrichment Analysis of up-regulated genes in hrPC12 cells.

Table S4. Pathway Enrichment Analysis of down-regulated REST potential targets.

Table S5. Pathway Enrichment Analysis of up-regulated REST potential targets.

Table S6. Transcription Factor Protein-Protein Interaction Network Enrichment Analysis of up-regulated genes.

  1. Supplementary Tables