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Series GSE197353 Query DataSets for GSE197353
Status Public on Feb 28, 2022
Title Spatial transcriptomic maps of whole mouse embryos
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Other
Summary Precise spatiotemporal orchestration of gene expression is required for proper embryonic development. The application of high throughput single-cell technologies have provided comprehensive transcriptomic definitions of cell states within the embryo, but our knowledge of their spatial localization remains elusive. To explore early mouse organogenesis, we used Slide-seq to generate high-resolution maps of whole E8.5 and E9.5 mouse embryos. We developed sc3D, a tool for creating a three-dimensional (3D) 'digital embryo,' which allowed us to quantitatively decipher regionalized gene expression across multiple tissues. Our transcriptomic atlas facilitated us to characterize gene expression patterns along the anteroposterior and dorsoventral axes, with a particular emphasis on neural tube development. We nominated and functionally characterized Prdm8, a histone methyltransferase, as a neural tube patterning gene. Furthermore, we were able to determine the transcriptional identity of ectopic neural tubes in a classical Tbx6 mutant, which provided us with additional insights into neural tube patterning. Taken together, we combined computational and experimental tools to generate a framework that enables systematic spatiotemporal dissection of complex embryonic structures via high-throughput profiling of molecular phenotypes, thereby paving the way for the investigation of congenital and developmental abnormalities.
 
Overall design Slide-seq v2 on whole mouse embryos E8.5 and E9.5 stage
 
Contributor(s) Sampath Kumar A, Tian L, Meissner A, Chen F
Citation(s) 37414952
Submission date Feb 24, 2022
Last update date Sep 12, 2023
Contact name Luyi Tian
E-mail(s) ltian@broadinstitute.org
Phone 8577779729
Organization name Broad institute
Lab Fei Chen Lab
Street address 415 main st Cambridge
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (23)
GSM5915040 E8.5_embryo_puck_201104_07
GSM5915041 E8.5_embryo_puck_201104_08
GSM5915042 E8.5_embryo_puck_201104_09
Relations
BioProject PRJNA810020

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
GSE197353_RAW.tar 1.5 Gb (http)(custom) TAR (of TAR, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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