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Series GSE175801 Query DataSets for GSE175801
Status Public on Nov 24, 2021
Title β-catenin, Tcf7l1, and Esrrb mediate seeding density-dependent gene regulation during mouse embryonic stem cell differentiation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Cell density affects numerous biological processes, including gene expression and cell fate specification. However, mechanistic understanding of how changes in cell density alter the transcriptome is lacking. Here, we reveal that the expression of thousands of genes in mouse embryonic stem cells is affected by cell density. Furthermore, we find that low cell density enhances the efficiency of differentiation. Mechanistically, β-catenin is localized primarily to adherens junctions during conditions of high cell-cell contact. At low seeding density during differentiation, we observe that β-catenin translocates to the nucleus and co-activates target genes in concert with Tcf7l1, leading to the induction of lineage markers. Meanwhile, Esrrb sustains the expression of high density-specific, pluripotency-associated genes, but low seeding density differentiation reduces its occupancy on its target loci. Our demonstration of factors that transcriptionally regulate genes responsive to cell density contributes to our understanding of gene regulation in stem cells and has implications for reproducibility, as density can vary between substantially labs and experimental protocols.
Overall design Expression and transcription factor occupancy in mouse embryonic stem cells at high and low cell seeding density.
Contributor(s) LeBlanc L, Kim J, Kim M
Citation(s) 34977504
Submission date May 30, 2021
Last update date Jan 10, 2022
Contact name Jonghwan Kim
Organization name University of Texas at Austin
Department Molecular Biosciences
Lab Kim Lab
Street address 2506 Speedway
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (67)
GSM5348196 ChIP-ES-betacatenin-lowdensity_r1
GSM5348197 ChIP-ES-betacatenin-lowdensity_r2
GSM5348198 ChIP-ES-Tcf7l1-input_r1
BioProject PRJNA733770
SRA SRP321923

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE175801_RAW.tar 92.3 Mb (http)(custom) TAR (of TSV, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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