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Series GSE59946 Query DataSets for GSE59946
Status Public on Aug 31, 2015
Title Epigenomics of neural cells: REST-induced down- and up-regulation of gene expression in a two clone PC12 cell model.
Organism Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary Cell epigenomics depends on the marks released by transcription factors operating via the assembly of complexes that induce focal changes of DNA and histone structure. Among these factors is REST, a repressor that, via its strong decrease, governs both neuronal and neural cell differentiation and specificity. REST operation on thousands of possible genes can occur directly or via indirect mechanisms including repression of other factors. In previous studies of gene down- and up-regulation, processes had been only partially investigated in neural cells. PC12 are well known neural cells sharing properties with neurons. In the widely used PC12 populations, low-REST cells coexist with few, spontaneous high-REST PC12 cells. High- and low-REST PC12 clones were employed to investigate the role and the mechanisms of the repressor action. Among 15,500 expressed genes we identified 1,770 target and non-target, RESTdependent genes. Functionally, these genes were found to operate in many pathways, from synaptic function to extracellular matrix. Mechanistically, downregulated genes were predominantly repressed directly by REST; up-regulated genes were mostly governed indirectly. Among other factors, Polycomb complexes cooperated with REST for down-regulation, Smad3 and Myod1 participated in up-regulation. In conclusion, we have highlighted that PC12 clones are a useful model to investigate REST, opening opportunities to development of epigenomic investigation.
Overall design 4 samples have been analyzed: 2 replicates from wtPC12 clone and 2 replicates from the hrPC12 clones
Contributor(s) Garcia-Manteiga JM, Bonfiglio S, Lazarevic D, Stupka E, Cittaro D, Meldolesi J, Malosio ML
Citation(s) 26413508
Submission date Jul 30, 2014
Last update date May 15, 2019
Contact name Jose Manuel Garcia-Manteiga
Organization name OSR - San Raffaele Scientific Institute
Department Center for Translational Genomics and Bioinformatics
Street address Via Olgettina 58
City Milan
State/province --
ZIP/Postal code 20132
Country Italy
Platforms (1)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
Samples (4)
GSM1462580 wt1
GSM1462581 wtb
GSM1462582 27a
BioProject PRJNA257108
SRA SRP045117

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Supplementary file Size Download File type/resource
GSE59946_RAW.tar 440.0 Kb (http)(custom) TAR (of TXT)
GSE59946_Supplementary_Table_1_statistical_analysis_allgenes.txt.gz 795.4 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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