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Series GSE216656 Query DataSets for GSE216656
Status Public on Mar 19, 2023
Title Transcription profiling of Smarce1- MD (R42A) and Smarce1- MD mESCs with BMP4 rescue.
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary To evaluate the effects of mitotic degradation of SMARCE1 upon gene expression, we performed RNA-sequencing (RNA-seq) of cultures of four independent subclones each of Smarce1-MD and control Smarce1-MD (R42A) mESCs. We found that transcription of the core pluripotency regulatory network was not disrupted. In contrast, GO analysis showed that neural differentiation-associated terms were enriched among genes upregulated in Smarce1-MD mESCs. To better understand the difference in neural fates in the neural induction experiments, we performed differential gene expression analysis and gene set enrichment analysis (GSEA) studies. Mitotic degradation of SMARCE1 resulted in higher expression of GABA receptors and hyper-activation of synaptic signaling on neural induction, indicating the aberrant neural cell fate commitment compared to SMARCE1-MD (R42A) cultures. And then we add back BMP4 to partically rescue the phenotype and very small amount of BMP4 will rescue the phenotype.
 
Overall design We performed RNA-seq in Smarce1- MD (R42A) and Smarce1- MD mESCs with different concentration of BMP4 rescue.
 
Contributor(s) ZHU Z, CHEN X
Citation(s) 37225980
Submission date Oct 26, 2022
Last update date Jun 02, 2023
Contact name Zhexin Zhu
E-mail(s) zhexin.zhu@gmail.com
Organization name St Jude Children's Research Hospital
Street address 262 Danny Thomas Pl
City Memphis
ZIP/Postal code 38105
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (24)
GSM6685370 Smarce1-MDR42A04_0ng_rep1
GSM6685371 Smarce1-MDR42A04_0.1ng_rep1
GSM6685372 Smarce1-MDR42A04_0.2ng_rep1
This SubSeries is part of SuperSeries:
GSE189563 Mitotic bookmarking by SWI/SNF subunits
Relations
BioProject PRJNA894701

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
GSE216656_RAW.tar 14.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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