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Series GSE253608 Query DataSets for GSE253608
Status Public on Jan 25, 2024
Title Primitive endoderm differentiation in wild-type and Med12-mutant mESCs [scRNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Cell differentiation results from coordinated changes in gene transcription in response to combinations of signals. FGF, Wnt, and mTOR signals regulate the differentiation of pluripotent mammalian cells towards embryonic and extraembryonic lineages, but how these signals cooperate with general transcriptional regulators is not fully resolved. Here, we report a genome-wide CRISPR screen that reveals both signaling components and general transcriptional regulators for differentiation-associated gene expression in mESCs. Focusing on the Mediator subunit Med12 as one of the strongest hits in the screen, we show that it regulates gene expression in parallel to FGF and mTOR signals. Loss of Med12 is compatible with differentiation along both the embryonic epiblast and the extraembryonic primitive endoderm lineage, but pluripotency transitions are slowed down, and the transcriptional separation between epiblast and primitive endoderm identities is enhanced in Med12-mutant cells. These cellular phenotypes correlate with reduced biological noise upon loss of Med12. These findings suggest that Med12 regulates cellular plasticity through the priming of transcriptional changes during differentiation, thereby modulating the effects of a broad range of signals.
Overall design Single cell sequencing of two Med12 wild-type and three independent Med12-mutant cell lines in the pluripotent state and after PrE differentiation. To minimize batch effects, samples were multiplexed and pooled before mRNA capture and library preparation
Contributor(s) Fernkorn M, Schröter C
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Submission date Jan 18, 2024
Last update date Jan 25, 2024
Contact name Max Fernkorn
Organization name Max Planck Institute of Molecular Physiology
Department Systemic Cell Biology
Street address Otto-Hahn-Strasse 11
City Dortmund
ZIP/Postal code 44225
Country Germany
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (2)
GSM8024055 Gene expression Library, multiplexed
GSM8024056 Cell multiplexing Library, multiplexed
This SubSeries is part of SuperSeries:
GSE253609 Med12 cooperates with multiple differentiation signals to enhance embryonic stem cell plasticity
BioProject PRJNA1066345

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
GSE253608_iG4_2iL_barcodes.tsv.gz 8.2 Kb (ftp)(http) TSV
GSE253608_iG4_2iL_features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSE253608_iG4_2iL_matrix.mtx.gz 23.3 Mb (ftp)(http) MTX
GSE253608_iG4_Dif_barcodes.tsv.gz 9.2 Kb (ftp)(http) TSV
GSE253608_iG4_Dif_features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSE253608_iG4_Dif_matrix.mtx.gz 32.4 Mb (ftp)(http) MTX
GSE253608_iG6_2iL_barcodes.tsv.gz 10.3 Kb (ftp)(http) TSV
GSE253608_iG6_2iL_features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSE253608_iG6_2iL_matrix.mtx.gz 29.5 Mb (ftp)(http) MTX
GSE253608_iG6_Dif_barcodes.tsv.gz 9.7 Kb (ftp)(http) TSV
GSE253608_iG6_Dif_features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSE253608_iG6_Dif_matrix.mtx.gz 33.9 Mb (ftp)(http) MTX
GSE253608_iG6_M12KO_A11_2iL_barcodes.tsv.gz 8.6 Kb (ftp)(http) TSV
GSE253608_iG6_M12KO_A11_2iL_features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSE253608_iG6_M12KO_A11_2iL_matrix.mtx.gz 28.6 Mb (ftp)(http) MTX
GSE253608_iG6_M12KO_A11_Dif_barcodes.tsv.gz 10.7 Kb (ftp)(http) TSV
GSE253608_iG6_M12KO_A11_Dif_features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSE253608_iG6_M12KO_A11_Dif_matrix.mtx.gz 37.1 Mb (ftp)(http) MTX
GSE253608_iG6_M12KO_A12_2iL_barcodes.tsv.gz 7.9 Kb (ftp)(http) TSV
GSE253608_iG6_M12KO_A12_2iL_features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSE253608_iG6_M12KO_A12_2iL_matrix.mtx.gz 25.0 Mb (ftp)(http) MTX
GSE253608_iG6_M12KO_A12_Dif_barcodes.tsv.gz 9.4 Kb (ftp)(http) TSV
GSE253608_iG6_M12KO_A12_Dif_features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSE253608_iG6_M12KO_A12_Dif_matrix.mtx.gz 33.1 Mb (ftp)(http) MTX
GSE253608_iG6_M12KO_A6_2iL_barcodes.tsv.gz 7.2 Kb (ftp)(http) TSV
GSE253608_iG6_M12KO_A6_2iL_features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSE253608_iG6_M12KO_A6_2iL_matrix.mtx.gz 22.5 Mb (ftp)(http) MTX
GSE253608_iG6_M12KO_A6_Dif_barcodes.tsv.gz 8.8 Kb (ftp)(http) TSV
GSE253608_iG6_M12KO_A6_Dif_features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSE253608_iG6_M12KO_A6_Dif_matrix.mtx.gz 29.6 Mb (ftp)(http) MTX
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