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Series GSE120963 Query DataSets for GSE120963
Status Public on Aug 08, 2019
Title Molecular architecture of lineage specification and tissue organization in early mouse embryo
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary During postimplantation development of the mouse embryo, descendants of the inner cell mass cells in the early epiblast transit from the naïve pluripotent state to the primed pluripotent state. Concurrent with the transition of the pluripotency states is the specification of cell lineages and formation of germ layers in the embryos that serves as the blueprint for embryogenesis. Fate mapping and lineage analysis studies have revealed that cells in different regions of the germ layers acquire location-specific cell fates during gastrulation. The regionalization of cell fates heralding the formation of the basic body plan is conserved in vertebrate embryos at a common phylotypic stage of development. Knowledge of the molecular regulation that underpin the lineage specification and tissue patterning is instrumental for understanding embryonic programming and stem cell-based translational study. However, a genome-wide molecular annotation of lineage segregation and tissue architecture of post-implantation embryo has yet to be undertaken. Here, we reported a spatially resolved transcriptome of cell populations at defined positions in the germ layers over the period of pre- to late gastrulation development. This spatio-temporal transcriptome provides high resolution digitized gene expression profiles and defines the molecular attribute of the genealogy of lineages and continuum of pluripotency states in time and space. The transcriptome further identifies the networks of molecular determinants that drive lineage specification and tissue patterning in the early postimplantation mouse embryo.
Overall design By using spatial transcriptome of Geo-seq, we carried out transcriptome profiling on embryo sections at a high resolution of 20-40 cells per sample. We then constructed a comprehensive spatial transcriptome map from the pre-gastrulation to late-gastrulation embryos that are visualized in a 3D embryonic model based on the sequencing data. Please be aware that the positions for left (L) and right (R) are from mirrored images and should be considered as right and left in real embryo settings. Anterior (A) or Posterior (P) regions do not change.
Web link
Contributor(s) Peng G, Cui G, Suo S, Jing N, Han JJ
Citation(s) 31391582
Submission date Oct 09, 2018
Last update date Aug 05, 2020
Contact name Guangdun Peng
Organization name Chinese Academy of Sciences
Department Guangzhou Institutes of Biomedicine and Health
Lab Stem cell and early development
Street address 190 Kaiyuan Road
City Guangzhou
ZIP/Postal code 510530
Country China
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (954)
GSM3422488 Stage E5.5 embryo 1 section 1 region AP (E5.5_1_1)
GSM3422489 Stage E5.5 embryo 1 section 2 region A (E5.5_1_2A)
GSM3422490 Stage E5.5 embryo 1 section 2 region P (E5.5_1_2B)
BioProject PRJNA495153
SRA SRP164676

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
GSE120963_E5.5_Embryo1_all.samples.genes.fpkm.txt.gz 406.5 Kb (ftp)(http) TXT
GSE120963_E5.5_Embryo2.ref.gene.fpkm.txt.gz 574.0 Kb (ftp)(http) TXT
GSE120963_E5.5_Embryo3Reference_all.samples.genes.fpkm.txt.gz 505.5 Kb (ftp)(http) TXT
GSE120963_E6.0_Embryo1_all.samples.genes.fpkm.txt.gz 469.7 Kb (ftp)(http) TXT
GSE120963_E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt.gz 600.0 Kb (ftp)(http) TXT
GSE120963_E6.0_Embryo3Reference_all.samples.genes.fpkm.txt.gz 856.6 Kb (ftp)(http) TXT
GSE120963_E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt.gz 1.2 Mb (ftp)(http) TXT
GSE120963_E6.5_Embryo2_all.samples.genes.fpkm.txt.gz 1.2 Mb (ftp)(http) TXT
GSE120963_E7.0SingleCell.tpm.txt.gz 15.9 Mb (ftp)(http) TXT
GSE120963_E7.0_Embryo1_all.samples.genes.fpkm.txt.gz 2.1 Mb (ftp)(http) TXT
GSE120963_E7.0_Embryo2_all.samples.genes.fpkm.txt.gz 2.2 Mb (ftp)(http) TXT
GSE120963_E7.0_Ref.all.combine.gene.fpkm.txt.gz 3.1 Mb (ftp)(http) TXT
GSE120963_E7.5_Embryo2_all.samples.genes.fpkm.txt.gz 2.9 Mb (ftp)(http) TXT
GSE120963_E7.5_Embryo3_all.samples.genes.revise.fpkm.txt.gz 2.6 Mb (ftp)(http) TXT
GSE120963_E7.5_Embyo1_all.samples.genes.fpkm.APLR.txt.gz 2.2 Mb (ftp)(http) TXT
GSE120963_E7.5_Ref_all.combine.gene.fpkm.txt.gz 3.9 Mb (ftp)(http) TXT
GSE120963_Invitro.endoderm.cluture.Yap.gene.fpkm.txt.gz 330.6 Kb (ftp)(http) TXT
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