GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE165002 Query DataSets for GSE165002
Status Public on Jan 18, 2021
Title Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Sequencing studies of autism spectrum disorder (ASD) cases have revealed a causal role for mutations to chromatin remodeling genes. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeler with one of the highest de novo mutation rates in sporadic ASD. However, the relationship between CHD8 genomic function and autism-relevant biology remains poorly elucidated. CHD8 binding studies have relied on Chromatin Immunoprecipitation followed by sequencing (ChIP-seq), but these datasets exhibit significant variation. ChIP-seq has technical limitations in the context of weak or indirect protein-DNA interactions or when high-performance antibodies are unavailable. Thus, complementary approaches are needed to establish CHD8 genomic targets. Here we used Targeted DamID in utero to characterize CHD8 binding activity in the developing embryonic mouse cortex. CHD8 Targeted DamID followed by sequencing (CHD8 TaDa-seq) revealed binding at previously identified genomic targets as well as at genes sensitive to Chd8 haploinsufficiency. CHD8 TaDa-seq showed greater sensitivity for CHD8 binding near a subset of genes specific to brain development and neuron function. These studies establish TaDa-seq as a useful alternative for mapping protein-DNA interactions in vivo and provide insights into the relationship between chromatin remodeling by CHD8 and autism-relevant pathophysiology associated with CHD8 mutations.
Overall design Targeted DamID sequencing of CHD8 binding loci via in utero electroporation of E17.5 mouse cortex.
Contributor(s) Wade AA, van den Ameele J, Cheetham SW, Yakob R, Brand AH, Nord AS
Citation(s) 34746699
Submission date Jan 17, 2021
Last update date Nov 10, 2021
Contact name Alex Nord
Phone 530-754-5022
Organization name University of California, Davis
Department Neurobiology, Physiology, & Behavior
Street address 1544 Newton Court
City Davis
State/province CA
ZIP/Postal code 95618
Country USA
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (7)
GSM5024307 CHD8 TaDa-seq Rep 1
GSM5024308 CHD8 TaDa-seq Rep 2
GSM5024309 CHD8 TaDa-seq Rep 3
BioProject PRJNA692752
SRA SRP302125

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 104.9 Mb (ftp)(http) BW 121.5 Mb (ftp)(http) BW
GSE165002_Dam-pCAG_merge.no_model_peaks.broadPeak.gz 3.4 Mb (ftp)(http) BROADPEAK
GSE165002_RAW.tar 414.3 Mb (http)(custom) TAR (of BROADPEAK, BW)
GSE165002_Versus_merge_5filter.bed_multrepsincluded.bed.gz 118.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap