Comment[ArrayExpressAccession]	E-GEOD-48314
MAGE-TAB Version	1.1			
Public Release Date	2013-08-26
Investigation Title	CHD5 is required for neurogenesis and has a dual role in facilitating gene expression and Polycomb gene repression			
Comment[Submitted Name]	CHD5 is required for neurogenesis and has a dual role in facilitating gene expression and Polycomb gene repression
Experiment Description	The chromatin remodeler CHD5 is expressed in neural tissue and is frequently deleted in aggressive neuroblastoma. Very little is known about the function of CHD5 in the nervous system or its mechanism of action. Here we report that depletion of Chd5 in the developing murine neocortex blocks neuronal differentiation and leads to an accumulation of undifferentiated progenitors. CHD5 binds a large cohort of genes and is required for facilitating the activation of neuronal genes. It also binds a cohort of Polycomb targets and is required for the maintenance of H3K27me3 on these genes. Interestingly, the chromodomains of CHD5 directly bind H3K27me3 and are required for neuronal differentiation. In the absence of CHD5, a subgroup of Polycomb-repressed genes becomes aberrantly expressed. These findings provide new insights into the regulatory role of CHD5 during neurogenesis and suggest how inactivation of this candidate tumor suppressor might contribute to neuroblastoma. Examination of genome-wide binding/occupancy of CHD5 in the SH-SY5Y cell line			
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl		
Person Last Name	Bracken	Egan	Bracken	
Person First Name	Adrian	Chris	Adrian	
Person Mid Initials	P.	M	P	
Person Email	geo@ncbi.nlm.nih.gov			
Person Affiliation	Trinity College Dublin			
Person Address	Department of Genetics, Trinity College Dublin, 1 Lincoln Place, Dublin, Ireland			
Person Roles	submitter			
Protocol Name	P-GSE48314-4	P-GSE48314-1	P-GSE48314-3	P-GSE48314-2
Protocol Description	Alignment; 50bp short reads were mapped onto the Human genome (hg19, Feb 2009) using the burrows-wheeler alignment tool, allowing for up to two mismatches in each read. Peak detection was performed using MACS (Zhang et al. 2008) where the FBio-Ctrl or Input_DNA datasets served as a normalization controls for the FBio-CHD5 and H3K27me3 datasets, respectively. Tag density files for each dataset were generated using the IGV toolkit. Genome_build: hg19, Feb 2009 Supplementary_files_format_and_content: tag density files	SH-SY5Y cells were treated for 8 days in the presence of 10uM Retinoic Acid (Media was changed on Days 2, 4, 6)	Differentiated SH-SY5Y cells cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin from FBio-CHD5 and Fbio-Ctrl expressing SH-SY5Y cells was precipitated with magnetic streptavidin beads (Invitrogen) or the H3K27me3 antibody and recovered DNA and an Input DNA control were used for high throughput sequencing. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 14 cycles and library fragments of 150-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was sent to BGI genomics for sequencing on an Illumina Hi-Seq 2000 platform.	SH-SY5Y cells were grown in DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol
Experimental Factor Name	EXPRESSION	CHIP ANTIBODY		
Experimental Factor Type	expression	chip antibody		
Comment[SecondaryAccession]	GSE48314			
Comment[GEOReleaseDate]	2013-08-26			
Comment[ArrayExpressSubmissionDate]	2013-06-26			
Comment[GEOLastUpdateDate]	2013-09-11			
Comment[AEExperimentType]	ChIP-seq			
Comment[AdditionalFile:Data1]	GSE48314_FBio_CHD5.peaks.bed			
Comment[AdditionalFile:Data2]	GSE48314_K27me3.peaks.bed			
Comment[SecondaryAccession]	SRP026335			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR922233-SRR922236			
SDRF File	E-GEOD-48314.sdrf.txt