NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE169210 Query DataSets for GSE169210
Status Public on Mar 20, 2021
Title A single embryo, single cell time-resolved model for mouse gastrulation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Mouse embryonic development is a canonical model system for studying mammalian cell fate acquisition. Recently, single-cell atlases comprehensively charted embryonic transcriptional landscapes, yet inference of the coordinated dynamics of cells over such atlases remains challenging. Here we introduce a temporal model for mouse gastrulation, consisting of data from 153 individually sampled embryos spanning 36 hours of molecular diversification. Using new algorithms and precise timing we infer differentiation flows and lineage specification dynamics over the embryonic transcriptional manifold. Rapid transcriptional bifurcations characterize the commitment of early specialized node and blood cells. However, for most lineages, we observe combinatorial multi-furcation dynamics rather than hierarchical transcriptional transitions. In the mesoderm, dozens of transcription factors combinatorially regulate multi-furcations, as we exemplify using time-matched chimeric embryos of Foxc1/Foxc2 mutants. Our study rejects the notion of differentiation being governed by a series of binary choices, providing an alternative quantitative model for cell fate acquisition.
 
Overall design Single cells from 153 WT mouse embryos (E6.5 - E8.25) were sequenced using MARS-seq2.0 which allowed to record each single cell's embryo identity during FACS cell-sorting. Using chimera and tetraploid complementation assays we analyzed the role of Foxc1 and Foxc2 during mesoderm specification. For both assays, we injected Foxc1/2 DKO and control cells into the blastocyst and performed scRNA-seq at ca. E7.5. Fluorescence intensity and embryo identity of each single cell from chimera and tetraploid embryos was recorded during FACS index-sorting.
 
Contributor(s) Mittnenzweig M, Mayshar Y, Cheng S, Ben-Yair R, Hadas R, Rais Y, Chomsky E, Reines N, Uzonyi A, Lumerman L, Lifshitz A, Mukamel Z, Orenbuch A, Tanay A, Stelzer Y
Citation(s) 33932341
Submission date Mar 19, 2021
Last update date Jun 09, 2021
Contact name Markus Mittnenzweig
E-mail(s) markus.mittnenzweig@weizmann.ac.il
Organization name Weizmann Institute of Science
Street address 234 Herzl St.
City Rehovot
State/province Shfela
ZIP/Postal code 7610001
Country Israel
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (154)
GSM5183637 wt_embryo_scRNA_seq_C57BL6 [181209_P01]
GSM5183638 wt_embryo_scRNA_seq_C57BL6 [181209_P03]
GSM5183639 wt_embryo_scRNA_seq_C57BL6 [181209_P04]
Relations
BioProject PRJNA715656
SRA SRP311334

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
GSE169210_RAW.tar 158.8 Mb (http)(custom) TAR (of TXT)
GSE169210_chimera_control_single_cell_metadata.txt.gz 123.4 Kb (ftp)(http) TXT
GSE169210_chimera_foxc12_dko_single_cell_metadata.txt.gz 197.7 Kb (ftp)(http) TXT
GSE169210_mixed_plate_single_cell_metadata.txt.gz 16.3 Kb (ftp)(http) TXT
GSE169210_tetraploid_control_single_cell_metadata.txt.gz 124.9 Kb (ftp)(http) TXT
GSE169210_tetraploid_foxc_dko_single_cell_metadata.txt.gz 125.0 Kb (ftp)(http) TXT
GSE169210_wt_bl6_single_cell_metadata.txt.gz 270.1 Kb (ftp)(http) TXT
GSE169210_wt_icr_single_cell_metadata.txt.gz 129.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap