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Series GSE101971 Query DataSets for GSE101971
Status Public on Sep 05, 2018
Title Targeted DamID reveals differential binding of mammalian pluripotency factors
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The precise control of gene expression by transcription factor networks is critical to organismal development. The predominant approach for mapping transcription factor-chromatin interactions has been chromatin immunoprecipitation (ChIP). However, ChIP requires a large number of homogeneous cells and antisera with high specificity. A second approach, DamID, has the drawback that high levels of Dam methylase are toxic. Here we modify our Targeted DamID approach (TaDa) to enable cell type-specific expression in mammalian systems, generating an inducible system (mammalian TaDa or MaTaDa) to identify protein/DNA interactions in 100 to 1000 times fewer cells than ChIP. We mapped the binding sites of key pluripotency factors, OCT4 and PRDM14, in mouse embryonic stem cells, epiblast-like cells and primordial germ cell-like cells (PGCLCs). PGCLCs are an important system to elucidate primordial germ cell development in mice. We monitored PRDM14 binding during the specification of PGCLCs, identifying direct targets of PRDM14 that are key to understanding its critical role in PGCLC development. We show that MaTaDa is a sensitive and accurate method to assess cell type specific transcription factor binding in limited numbers of cells.
Overall design MaTaDa of OCT4 and PRDM14 in ESCs, EpiLCs and PGCLCs
Contributor(s) Cheetham SW, Gruhn WH, van den Ameele J, Krautz R, Southall TD, Kobayashi T, Surani MA, Brand AH
Citation(s) 30185410
Submission date Jul 27, 2017
Last update date May 15, 2019
Contact name Andrea Brand
Organization name The Gurdon Institute
Street address Tennis Court Rd
City Cambridge
ZIP/Postal code CB2 1QN
Country United Kingdom
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (32)
GSM2719804 dam_gfp_esc1
GSM2719805 dam_gfp_esc2
GSM2719806 dam_gfp_esc3
BioProject PRJNA396044
SRA SRP113712

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Supplementary file Size Download File type/resource
GSE101971_oct4_matada_epilc_average.bedgraph.gz 48.8 Mb (ftp)(http) BEDGRAPH
GSE101971_oct4_matada_esc_average.bedgraph.gz 51.7 Mb (ftp)(http) BEDGRAPH
GSE101971_prdm14_matada_esc_10000.bedgraph.gz 51.4 Mb (ftp)(http) BEDGRAPH
GSE101971_prdm14_matada_esc_average.bedgraph.gz 52.1 Mb (ftp)(http) BEDGRAPH
GSE101971_prdm14_matada_pgclc_average.bedgraph.gz 53.7 Mb (ftp)(http) BEDGRAPH
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