Comment[GEAAccession]	E-GEAD-465
MAGE-TAB Version	1.1
Investigation Title	PFC extinction in early life stress model mice
Experiment Description	We aim to understand 1) how the spatial gene expression pattern in medial prefrontal cortex changes after early life stress (HC_SI) and 2) if each projection-specific population of prefrontal cortex has unique gene expression after the extinciton (Ext_SI).
Experimental Design	sex design	stimulus or stress design
Experimental Factor Name	condition
Experimental Factor Type	condition
Person Last Name	Uematsu	Sazhina	Sequence
Person First Name	Akira	Tatiana	Kashiwa
Person Affiliation	The University of Tokyo		
Person Roles	submitter	submitter	submitter
Public Release Date	2025-11-26
Protocol Name	P-GEAD-1009	P-GEAD-1010	P-GEAD-1011	P-GEAD-1012	P-GEAD-1013
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	All mice were socially isolated for 2weeks. The Ext_SI group was subjected to fear conditioning and extinciton, while HC_SI group was remained in their home cage. Mice were decapitutated and brain tissues were snap frozen in a bath of isopentane and liquid nitrogen. After these steps, we followed the Visium protocols (CG000240&CG000312) except for skipping the primary and secondary antibody stainings.	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(90 bp).	Sequence data was processed by Space Ranger v1.2.1(10x Genomics). Slide information; 1_M1F1_HC_SI:slide=V10N12-128,area=A1,2_M3F2_Ext_SI:slide=V10N12-128,area=B1,3_M4F4_HC_SI:slide=V10N12-128,area=C1,4_M6F5_Ext_SI:slide=V10N12-128,area=D1
SDRF File	E-GEAD-465.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB12669
Comment[Last Update Date]	2025-11-26