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Series GSE65924 Query DataSets for GSE65924
Status Public on Mar 24, 2016
Title Stereo-sequencing: 3D Transcriptome of the mouse embryo at gastrulation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary To glean an appreciation of the holistic genetic activity in the gastrulating mouse embryo, we performed a genome-wide spatial transcriptome analysis (Stereo-seq), using a low-cell number sequencing protocol on laser microdissected samples of epiblast cells with retained positional address. The 3D transcriptome reveals that (i) the epiblast is partitioned into transcription domains corresponding to regions of epiblast where cells are endowed specifically with ectoderm and mesendoderm potency, (ii) novel lineage markers are identified as genes expressed in epiblast domains populated by cells displaying different lineage fates, (iii) functionally related gene regulatory circuitry and signaling pathways are acting in concert in the transcriptional domains, and (iv) the spatial information provides reference zipcodes for mapping the prospective address of cell samples from different embryos and stem cell lines. The quantified expression data can also be visualized as “3D digitized whole mount in situ hybridization” of all the expressed transcripts in the epiblast.
Overall design (i) By using laser-microdissection, we carried out transcriptome profiling on embryo sections at a high resolution of ~20 cells per sample with the spatial information preserved. We then constructed a comprehensive spatial transcriptome map in the mid-gastrulation embryo that is visualized in a 3D embryonic model based on the sequencing data.
Embryo position (A/L/P/R) and section (1-11) descriptors:
A stands for laser capture microdissected samples from the anterior epiblast of the embryo; P for posterior; L for the left lateral epiblast of the embryo; R for the right lateral. The section is collected from distal to proximal, and the section 1 to 11 is the cryosection order, covering the whole embryonic part of a late mid-streak embryo. Section 1 is the most distal section and 11 is the most proximal section. Please be aware that the labels for left (L) and right (R) are from mirrored images and should be considered as right and left positions in real embryo settings. Anterior (A) or Posterior (P) regions do not change.
(ii) Additional samples are RNA-seq data of 70 single cells from E7.0 mouse embryo. These 70 samples were randomly picked from the anterior or posterior embryonic half.
Web link,
Contributor(s) Peng G, Suo S, Chen J, Jing N, Han JJ
Citation(s) 27003939
Submission date Feb 13, 2015
Last update date Aug 11, 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 (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (192)
GSM1611141 Embryo 1 section 1 position A
GSM1611142 Embryo 1 section 1 position P
GSM1611143 Embryo 1 section 2 position A
BioProject PRJNA275415
SRA SRP055019

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Supplementary file Size Download File type/resource
GSE65924_E1.gene.expression.txt.gz 1.8 Mb (ftp)(http) TXT
GSE65924_E1_mapping.ratio.xlsx 17.7 Kb (ftp)(http) XLSX
GSE65924_E2.gene.expression.txt.gz 1.9 Mb (ftp)(http) TXT
GSE65924_E2_mapping.ratio.xlsx 17.7 Kb (ftp)(http) XLSX
GSE65924_E3.gene.expression.txt.gz 2.1 Mb (ftp)(http) TXT
GSE65924_E3_mapping.ratio.xlsx 26.2 Kb (ftp)(http) XLSX
GSE65924_E7.0.single.cell.gene.expression.txt.gz 2.2 Mb (ftp)(http) TXT
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