Comment[GEAAccession]	E-GEAD-393
MAGE-TAB Version	1.1
Investigation Title	Spatial gene expression profiles in the mouse developing heart using Visum
Experiment Description	This study aimed to clarify the characteristics of cardiac neural crest cells during heart development at the spatiotemporal level. Embryonic hearts from E14.5 and E17.5 Wnt1-Cre; R26-EYFP mice, which label neural crest-derived cells, were used to analyze the spatial transcriptomics by using the technology of Visium. The result reveals the spatiotemporal gene expression profiles originated from the approximately 5000 spots per section. Adjusting the gene expression matrices to each HE-stained sample clarifies the difference of cell characteristics depending on the histology. Furthermore, the analysis of transcriptomic spot data is expected to reveal the continuity of cell differentiation based on the histological validation.
Experimental Design	cell component comparison design	cell type comparison design	development or differentiation design	time series design
Experimental Factor Name	mouse embryonic day
Experimental Factor Type	mouse embryonic day
Person Last Name	IWASE	KURIHARA	Sequence
Person First Name	Akiyasu	Hiroki	Kashiwa
Person Affiliation	The University of Tokyo		
Person Roles	submitter		
Public Release Date	2024-09-01
Protocol Name	P-GEAD-626	P-GEAD-627	P-GEAD-628	P-GEAD-629	P-GEAD-630
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Wnt1-Cre; R26-EYFP mouse embryonic hearts at E14.5 and E17.5 were embedded in OCT compound. The embedded tissues were cut into 10 um sections by cryostat. The cryosections were subjected to HE staining, RNA extraction, and cDNA synthesis by using Visium Spatial Gene Expression technology.	Visium Spatial Gene Expression Reagent Kits(10x Genomics)	The sequence library was constructed using the Visium Spatial Gene Expression Reagent Kits(10x Genomics).	Sequencing was performed on the Illumina NovaSeq6000 in paired end mode; Read1:Spatial Barcode, UMI(28 bp), i7 Index:Sample Index(10 bp), i5 Index:Sample Index(10 bp), Read2:Insert(120 bp).	Sequence data was processed by Space Ranger(10x Genomics).  Slide information; 1_E14_5_1:slide=V19N20-049,area=A1, 2_E14_5_2:slide=V19N20-049,area=B1, 3_E17_5_1:slide=V19N20-049,area=C1, 4_E17_5_2:slide=V19N20-049,area=D1
SDRF File	E-GEAD-393.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB10486
Comment[Last Update Date]	2026-07-21