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Series GSE113671 Query DataSets for GSE113671
Status Public on Nov 18, 2019
Title NELFA is a novel regulator of the 2C-like state
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Mouse embryonic stem cells (mESCs) are not homogenous; a rare subpopulation of cells can sporadically transit into a early-embryonic-like state and exhibits a gene expression program resembling that of the 2-cell (2C) embryo. We identified the maternal factor NELFA as a novel driver of the 2C-like gene expression through multiple mechanisms. We further demonstrate that the entry of mESCs into the 2C-like state is accompanied by epigenetic and metabolic reprogramming, and that perturbation of the metabolic state via a small molecule can promote this cell fate reversion in a NELFA-dependent manner, obviating the need for any genetic manipulation. Our findings thus place NELFA as one of the earliest regulators of 2C gene expression, extending contemporary knowledge of how totipotency may be regulated.
 
Overall design To compare the gene expression differences between NELFAhigh and NELFAlow mESCs, we generated both a NELFA-StrepHA-P2A-EGFP reporter and a Dox-inducible NELFA- StrepHA-P2A-EGFP mESC stable line. The NELFA-reporter mESCs was treated with 4mM 2-DG for 4 days before harvesting total RNA for unbiased transcriptomic analysis with RNA-Seq, while Dox-inducible NELFA was induced with 0.4 µg/ml of Dox for 16 hours before FACS enrichment for both GFP positive and negative populations for RNA-seq, with an additional ERCC spike-in included in library preparation for normalization purposes in the downstream analysis for those two experiments. Both NELFA reporter and Dox-inducible mESCs were cultured in standard ESC media containing serum, LIF and 2i; briefly, knockout DMEM was supplemented with 15% FCS, L-Glutamine, non-essential amino acids, penicillin/streptomycin, 2-mercaptoethanol and supplemented with LIF, 1 µM PD0325901 and 3 µM CHIR99021.
 
Contributor(s) Hu Z, Kiat TE, Bin CL, Jieming C, Leong H, Tee W, Lau M, Tan H
Citation(s) 31932739
Submission date Apr 25, 2018
Last update date Feb 18, 2020
Contact name Zhenhua hu
E-mail(s) zhhu@imcb.a-star.edu.sg
Phone 65869644
Organization name IMCB, A*STAR
Street address 31 Biopolis drive
City Singapore
State/province singapore
ZIP/Postal code 138673
Country Singapore
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (35)
GSM3110917 RNA-seq.Sorted-GFPpos-rep1
GSM3110918 RNA-seq.Sorted-GFPneg-rep1
GSM3110919 RNA-seq.Sorted-GFPpos-rep2
Relations
BioProject PRJNA453559
SRA SRP142615

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Supplementary file Size Download File type/resource
GSE113671_2DGminus_ATAC.bw 407.4 Mb (ftp)(http) BW
GSE113671_2DGplus_ATAC.bw 407.4 Mb (ftp)(http) BW
GSE113671_ATAC-seq_condition_specific_regions.xlsx 3.0 Mb (ftp)(http) XLSX
GSE113671_NELFA_ChIP_peaks.narrowPeak.gz 949.5 Kb (ftp)(http) NARROWPEAK
GSE113671_RNA-seq.xlsx.gz 16.0 Mb (ftp)(http) XLSX
GSE113671_mNELFA_DOXminu_ATAC.bw 380.3 Mb (ftp)(http) BW
GSE113671_mNELFA_DOXplus_ATAC.bw 389.2 Mb (ftp)(http) BW
GSE113671_mNELFA_DOXplus_ChIP_IP.bw 513.4 Mb (ftp)(http) BW
GSE113671_mNELFA_DOXplus_ChIP_input.bw 455.2 Mb (ftp)(http) BW
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Processed data are available on Series record

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