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Series GSE93524 Query DataSets for GSE93524
Status Public on Aug 17, 2017
Title Antagonistic activities of Sox2 and Brachyury control the fate choice of neuro-mesodermal progenitors
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The spinal cord and mesodermal tissues of the trunk such as the vertebral column and skeletal musculature derive from neuro-mesodermal progenitors (NMPs). Sox2, Brachyury (T) and Tbx6 have been correlated with NMP potency and lineage choice, however, their exact role and interaction in these processes have not been revealed yet. Here we present a global analysis of NMPs and their descending lineages performed on purified cells from E8.5 wild-type and mutant embryos. We show that T, cooperatively with WNT signaling, controls the progenitor state and the switch towards the mesodermal fate. Sox2 acts antagonistically and promotes neural development. Tbx6 reinforces the mesodermal fate choice, represses the progenitor state and confers paraxial fate commitment. Our findings refine previous models and establish new concepts of the molecular principles of mammalian trunk development comprising NMP maintenance, lineage choice and mesoderm formation.
Overall design Bulk transcriptomes (RNA-Seq) and chromatin accessibility (ATAC-Seq) from T/Sox2 expressing subpopulations isolated during trunk development from wildtype and T knock-out mouse embryos. Data is supplemented by Fluidigm single-cell RNA-Seq for T/Sox2 co-expressing cells from wildtype embryos and a bulk RNA-Seq comparison of wildtype and Tbx6 knock-out mouse embryos. ChIP-Seq for T, Sox2, Tbx6 and beta-catenin has been performed with chromatin from in vitro differentiated neuromesodermal progenitors and presomitic mesoderm.
Contributor(s) Koch F, Scholze M, Wittler L, Schifferl D, Sudheer S, Grote P, Timmermann B, Macura K, Herrmann BG
Citation(s) 28826820
Submission date Jan 11, 2017
Last update date Jul 25, 2021
Contact name Frederic Koch
Organization name Max Planck Institute for Molecular Genetics
Department Developmental Genetics
Street address Ihnestra├če 63-73
City Berlin
ZIP/Postal code 14195
Country Germany
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (79)
GSM2454124 ATAC S+ KO TS12
GSM2454125 ATAC S+ KO TS13
GSM2454126 ATAC S+ WT TS12
BioProject PRJNA360989
SRA SRP096588

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
GSE93524_FPKM_NMP.txt.gz 261.2 Kb (ftp)(http) TXT
GSE93524_FPKM_SingleCell.txt.gz 1.6 Mb (ftp)(http) TXT
GSE93524_FPKM_T_Tbx6_KO.txt.gz 463.0 Kb (ftp)(http) TXT
GSE93524_RAW.tar 4.1 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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