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Series GSE178390 Query DataSets for GSE178390
Status Public on May 19, 2022
Title Cell cycle states of pluripotent cells dictate lineage decisions
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Cell cycle and differentiation decisions are tightly linked; however, the underlying principles that drive these decisions are not fully understood. Here, we combined cell-cycle reporter system and single-cell RNA-seq profiling, to study the transcriptomes of mouse embryonic stem cells (ESCs) in the context of cell cycle states and differentiation. By applying a retinoic acid-based differentiation protocol we show that only cells in the G2/M phase are capable of differentiating into extraembryonic endoderm cells (XENs), whereas cells in the G1 phase predominantly produce epiblast stem cells (EpiSCs). Mechanistically, we show that Esrrb is a potent XEN state inducer as it is predominantly upregulated during G2/M phase, and cells engineered to overexpress Esrrb during G1 phase forced the cells to become XENs. Interestingly, this phenomenon is unique to the pluripotency ground state as sorting cells after 48 hours of differentiation resulted in a cell cycle-independent differentiation decisions. Cells in both G1 and G2/M phases contributed equally to EpiSC and XEN cellular lineages. Taken together, this study reveals an important functional link between cell-cycle states of pluripotent cells and lineage decisions, emphasizing the regulatory role of cell cycle during exit from pluripotency and can be further expand our understanding of early differentiation events.
Overall design We used R1 mESC line, each experiment includes technical duplicats.we established R1 clones with Fucci, sorted according to cell cycle stage at 0, 2 , 4 days of RA differentiation - then bulk or single cell analysis. We also used R1-fucci-Over expression ESRRB cells and zhbtc4 esrrb KO cells and preformes single cell analysis on them.
Contributor(s) Herchcovici Levy S, Arnon L, Feldman S, Alajem A, Awawdy M, Lahav S, Bavli D, Sun X, Buganim Y, Ram O
Citation(s) 35594859
Submission date Jun 17, 2021
Last update date Jun 30, 2022
Contact name Muhammad Awawdy
Phone +972528482707
Organization name Hebrew university of jerusalem
Lab Muhammad Awawdy
Street address The Hebrew University, The Edmond J. Safra Campus - Givat Ram
City jerusalem
ZIP/Postal code 9190401
Country Israel
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21626 NextSeq 550 (Mus musculus)
Samples (65)
GSM5389548 R1C1 4D RA early G1 rep1
GSM5389549 R1C1 4D RA early G1 rep2
GSM5389550 R1C1 4D RA G2 rep 1
BioProject PRJNA738859
SRA SRP324494

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
GSE178390_RAW.tar 130.0 Mb (http)(custom) TAR (of BED, RESULTS)
GSE178390_chipK4me1_KOES_Promoters.bed.gz 1.6 Mb (ftp)(http) BED
GSE178390_chipK4me1_WTES_Promoters.bed.gz 1.5 Mb (ftp)(http) BED
GSE178390_chipK4me2_KOES_Enhancers.bed.gz 808.6 Kb (ftp)(http) BED
GSE178390_chipK4me2_KOES_Promoters.bed.gz 1.8 Mb (ftp)(http) BED
GSE178390_chipK4me2_WTES_Enhancers.bed.gz 808.0 Kb (ftp)(http) BED
GSE178390_chipK4me2_WTES_Promoters.bed.gz 1.9 Mb (ftp)(http) BED
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Raw data are available in SRA
Processed data provided as supplementary file

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