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Series GSE56876 Query DataSets for GSE56876
Status Public on Oct 16, 2014
Title Arid3a modulates the first cell fate decision by direct regulation of both embryonic and extraembryonic gene expression (ChIP-Seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Arid3a, a transcription factor known for its requirement in B-lymphocyte development, has been recently identified as a member of ES cell pluripotency network. Arid3a is moderately expressed in ES cells, and its expression is gradually increased during differentiation. Since Arid3a shows the highest expression in placenta, we hypothesized that Arid3a may play important roles in TE development. We report that Arid3a is a central regulator of both TE-specific and pluripotency-associated gene expression during ES cell differentiation. While dispensable for self-renewal, we observed that knockdown of Arid3a delays differentiation of ES cells. Induction of Arid3a leads ES cells to promote differentiation, specifically towards TE lineage. Moreover, these Arid3a-overexpressing cells maintained in TE culture media are sufficient to generate functional trophoblast stem-like cells, suggesting roles of Arid3a in TE differentiation. By integrative analyses using the chromosomal targets of Arid3a with expression profiling, we revealed the dual roles of Arid3a, as a direct activator of TE-specific genes and a repressor of pluripotency-associated genes. We further revealed the repressive roles of Arid3a are mediated by histone deacetylases (HDACs). Taken together, our results demonstrate that Arid3a is a critical novel regulator in TE lineage specification.
Overall design Arid3a ChIP was performed using bioChIP-sequencing. Control ChIP-sequencing was performed using BirA cells. HDAC1 ChIP was performed as native antibody ChIP-sequencing.
Contributor(s) Kim J
Citation(s) 25319825
Submission date Apr 17, 2014
Last update date May 15, 2019
Contact name Jonghwan Kim
Phone 512-232-8046
Organization name University of Texas at Austin
Department Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology
Lab Kim Lab
Street address 2506 Speedway NMS 4.246
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (7)
GSM1370509 Arid3a OE-High
GSM1370510 Arid3a OE-Low
GSM1370511 BirA control
This SubSeries is part of SuperSeries:
GSE56877 Arid3a is essential to execution of the first cell fate decision via direct embryonic and extraembryonic transcriptional regulation
BioProject PRJNA244859
SRA SRP041250

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
GSE56876_RAW.tar 940.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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