GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE67673 Query DataSets for GSE67673
Status Public on Sep 21, 2015
Title Genome-wide map of H3K4me3 in HEK293 cells after PRDM9 expression
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary PRDM9 is a histone methyltransferase expressed in meiotic germ cells that determines the location of genetic recombination hotspots through binding of its allele-specific DNA binding domain. Here we characterize the genome-wide chromatin modification for two human PRDM9 alleles (A and C) in human cell lines. HEK293 cells were transfected with both alleles and an empty vector control. Resulting chromatin was subjected to H3K4me3 ChIP followed by high-throughput sequencing. We find that different PRDM9 allele largely modified chromatin in entirely different genomic regions in somatic cells determined by the protein's zinc-finger DNA binding domains. Many of the allele-specific peaks overlap sites of meiotic double-strand breaks found in vivo in human germ cells suggesting that transient expression of PRDM9 in somatic cells can reflect binding in vivo.
Overall design Identify PRDM9-dependent H3K4me3 sites by comparing modified chromatin after expression of different human PRDM9 alleles in HEK293 cells.
Contributor(s) Baker CL, Paigen K
Citation(s) 26368021
Submission date Apr 08, 2015
Last update date May 15, 2019
Contact name Christopher Lee Baker
Phone 2072886365
Organization name The Jackson Laboratory
Department Research
Street address 600 Main Street
City Bar Harbor
State/province ME
ZIP/Postal code 04609
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (10)
GSM1653246 Empty_Vector_H3K4me3_Input
GSM1653247 Empty_Vector_H3K4me3_ChIP
GSM1653248 PRDM9C_H3K4me3_Input
BioProject PRJNA280610
SRA SRP057026

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
GSE67673_RAW.tar 1.3 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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