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Series GSE228590 Query DataSets for GSE228590
Status Public on Apr 07, 2023
Title A single-cell time-lapse of mouse prenatal development from gastrula to birth
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The house mouse, Mus musculus, is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates the astonishing transformation of a single cell zygote into a free-living pup composed of >500 million cells.
Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediately postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types, and perform deeper dives into the unfolding of the posterior embryo during somitogenesis, as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons.
Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to curate a data-driven pseudotree of mouse development from zygote to pup (E0 to P0). Throughout this pseudotree, we systematically nominate sets of transcription factors (TFs) as candidate drivers of the in vivo differentiation of hundreds of mammalian cell types.
Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life.
 
Overall design In brief, 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediately postpartum period.
 
Contributor(s) Qiu C, Martin BK, Welsh IC, Daza RM, Huang X, Nichols E, Taylor M, Fulton O, Le T, O'Day DR, Gomes AR, Ilcisin S, Srivatsan S, Hamazaki N, Deng X, Disteche CM, Noble WS, Cao J, Spielmann M, Moens CB, Kimelman D, Schier AF, Murray SA, Trapnell C, Shendure J
Citation(s) 38355799
Submission date Mar 30, 2023
Last update date Feb 15, 2024
Contact name Chengxiang Qiu
E-mail(s) cxqiu@uw.edu
Organization name University of Washington
Department Genome Sciences
Lab Jay Shendure
Street address William H. Foege Hall, 3720 15th Ave NE
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL30172 NextSeq 2000 (Mus musculus)
Samples (9024)
GSM7124483 run_13_seq_1_PA-01A_S1
GSM7124484 run_13_seq_1_PA-01B_S2
GSM7124485 run_13_seq_1_PA-01C_S3
Relations
BioProject PRJNA950412
SRA SRP430180

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
GSE228590_cell_annotation.run_13.csv.gz 4.6 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_14.csv.gz 5.3 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_15.csv.gz 4.8 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_16.csv.gz 4.9 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_17_sub1.csv.gz 2.8 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_17_sub2.csv.gz 3.3 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_18.csv.gz 4.7 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_19.csv.gz 5.4 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_20.csv.gz 5.0 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_21.csv.gz 2.2 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_22.csv.gz 3.9 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_23.csv.gz 2.4 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_24.csv.gz 2.9 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_25.csv.gz 9.3 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_26.csv.gz 2.7 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_27.csv.gz 2.4 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_28.csv.gz 6.1 Mb (ftp)(http) CSV
GSE228590_cell_annotation.run_29.csv.gz 518.7 Kb (ftp)(http) CSV
GSE228590_cell_annotation.run_4.csv.gz 745.5 Kb (ftp)(http) CSV
GSE228590_gene_annotation.csv.gz 925.9 Kb (ftp)(http) CSV
GSE228590_gene_count.run_13.mtx.gz 3.5 Gb (ftp)(http) MTX
GSE228590_gene_count.run_14.mtx.gz 4.9 Gb (ftp)(http) MTX
GSE228590_gene_count.run_15.mtx.gz 4.0 Gb (ftp)(http) MTX
GSE228590_gene_count.run_16.mtx.gz 4.2 Gb (ftp)(http) MTX
GSE228590_gene_count.run_17_sub1.mtx.gz 2.9 Gb (ftp)(http) MTX
GSE228590_gene_count.run_17_sub2.mtx.gz 3.4 Gb (ftp)(http) MTX
GSE228590_gene_count.run_18.mtx.gz 4.2 Gb (ftp)(http) MTX
GSE228590_gene_count.run_19.mtx.gz 4.7 Gb (ftp)(http) MTX
GSE228590_gene_count.run_20.mtx.gz 4.7 Gb (ftp)(http) MTX
GSE228590_gene_count.run_21.mtx.gz 2.1 Gb (ftp)(http) MTX
GSE228590_gene_count.run_22.mtx.gz 3.8 Gb (ftp)(http) MTX
GSE228590_gene_count.run_23.mtx.gz 1.7 Gb (ftp)(http) MTX
GSE228590_gene_count.run_24.mtx.gz 2.7 Gb (ftp)(http) MTX
GSE228590_gene_count.run_25.mtx.gz 5.7 Gb (ftp)(http) MTX
GSE228590_gene_count.run_26.mtx.gz 2.3 Gb (ftp)(http) MTX
GSE228590_gene_count.run_27.mtx.gz 1.8 Gb (ftp)(http) MTX
GSE228590_gene_count.run_28.mtx.gz 2.5 Gb (ftp)(http) MTX
GSE228590_gene_count.run_29.mtx.gz 163.9 Mb (ftp)(http) MTX
GSE228590_gene_count.run_4.mtx.gz 1.6 Gb (ftp)(http) MTX
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