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Series GSE25409 Query DataSets for GSE25409
Status Public on Dec 23, 2010
Title Role of Prdm14 in mouse embryonic stem cells: ChIP-seq and RNA-seq analyses
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Prdm14 is a PR-domain and zinc-finger protein whose expression is restricted to the pluripotent cells of an early embryo, embryonic stem cells (ESCs), and germ cells. Here we show that Prdm14 safeguards mouse ESC maintenance by preventing induction of extraembryonic endoderm (ExEn) fates. Conversely, Prdm14 overexpression impairs ExEn differentiation during embryoid body (EB) formation. Prdm14 occupies and represses genomic loci encoding ExEn differentiation factors, while also binding to and promoting expression of genes associated with ESC self-renewal. Prdm14-bound genomic regions significantly overlap those occupied by Nanog and Oct4, are enriched in a chromatin signature associated with distal regulatory elements, and contain a unique DNA-sequence motif recognized by Prdm14 in vitro. Our work identifies Prdm14 as a new member of mouse ESC (mESC) transcriptional network, which plays a dual role as a context-dependent transcriptional repressor or activator at distal silencers and enhancers.
 
Overall design [ChIP-seq] Genome-wide mapping of Prdm14 binding sites in mouse embryonic stem cells:
A FLAG-HA tagged Prdm14 (FH-Prdm14) mESC line was established. FLAG-HA double ChIP (ChIP with FLAG antibody followed by ChIP with HA antibody) was performed with FH-Prdm14 mESCs (Prdm14-ChIPseq) and as a negative control, wildtype mESCs (FLAG-HA_ChIPseq).
H3K4me1 ChIPseq in mouse ES cells. Using published H3K4me1 data, we found there is a correlation between Prdm14 binding and H3K4me1 marks. So we obtained our own H3K4me1 data, using the wildtype mESCs.

[RNA-seq] Global RNAseq analysis of Prdm14 knockdown in mouse embryonic stem cells:
Analysis of poly(A)+ RNA from mESCs treated with non-targeting control siRNA and Prdm14 siRNA.
 
Contributor(s) Ma Z, Wysocka J
Citation(s) 21183938
Submission date Nov 16, 2010
Last update date May 15, 2019
Contact name Ziyang Ma
E-mail(s) ziyangm@gmail.com
Organization name Stanford University
Street address 269 Campus Dr, Room 3130
City Stanford
ZIP/Postal code 94305
Country USA
 
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (6)
GSM623989 Prdm14_ChIPseq
GSM623990 FLAG-HA_ChIPseq
GSM623991 Input_DNA_sequencing_ChIPseq (control)
Relations
SRA SRP004451
BioProject PRJNA134151

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
GSE25409_RAW.tar 1.3 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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