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Series GSE195545 Query DataSets for GSE195545
Status Public on Aug 24, 2022
Title Hypoxia induces an early primitive streak signature, enhancing spontaneous elongation and lineage representation in gastruloids
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The cellular microenvironment together with intrinsic regulators shapes stem cell identity and differentiation capacity. Mammalian early embryos are exposed to hypoxia in vivo and appear to benefit from hypoxic culture in vitro. Yet, how hypoxia influences stem cell transcriptional networks and lineage choices remain poorly understood. Here we investigated the molecular effects of acute and prolonged hypoxia on embryonic and extraembryonic stem cells as well as the functional impact on differentiation potential. We find a temporal and cell type-specific transcriptional response including an early primitive streak signature in hypoxic embryonic stem cells (ESCs) mediated by HIF1. Using a 3D gastruloid differentiation model, we show that hypoxia-induced T expression enables symmetry breaking and axial elongation in the absence of exogenous WNT activation. When combined with exogenous WNT activation, hypoxia enhances lineage representation in gastruloids, as demonstrated by highly enriched signatures of gut endoderm, notochord, neuromesodermal progenitors and somites. Our findings directly link the microenvironment to stem cell function and provide a rationale supportive of applying physiological conditions in models of embryo development.
 
Overall design Examination of Hif1a binding sites in acute (2 days) and in prolonged (6 days) hypoxia in ES cells.
 
Contributor(s) Lopez-Anguita N, Gassaloglu SI, Stötzel M, Bolondi A, Conkar D, Typou M, Buschow R, Veenvliet J, Bulut-Karslioglu A
Citation(s) 36102628
Submission date Jan 27, 2022
Last update date Nov 17, 2022
Contact name Natalia Lopez-Anguita
E-mail(s) anguita@molgen.mpg.de
Organization name Max Planck Institute for Molecular Genetics
Department Genome Regulation
Lab Bulut-Karslioglu Lab
Street address Ihnestraße 63
City Berlin
State/province Berlin
ZIP/Postal code 14195
Country Germany
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (8)
GSM5840323 hif1a_hyp_d2_br1
GSM5840324 hif1a_hyp_d2_br2
GSM5840325 hif1a_hyp_d6_br1
This SubSeries is part of SuperSeries:
GSE178628 Hypoxia induces an early primitive streak signature, enhancing spontaneous elongation and lineage representation in gastruloids
Relations
BioProject PRJNA801223

Download family Format
SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE195545_Hif1a_hypD2_merged.sorted.bam.cov.CPM.smooth.bw 300.4 Mb (ftp)(http) BW
GSE195545_Hif1a_hypD6_merged.sorted.bam.cov.CPM.smooth.bw 295.0 Mb (ftp)(http) BW
GSE195545_Hif1a_norm_merged.sorted.bam.cov.CPM.smooth.bw 293.1 Mb (ftp)(http) BW
GSE195545_Input_merged.sorted.bam.cov.CPM.smooth.bw 278.6 Mb (ftp)(http) BW
GSE195545_RAW.tar 270.0 Kb (http)(custom) TAR (of NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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