Comment[GEAAccession]	E-GEAD-434
MAGE-TAB Version	1.1
Investigation Title	PFC extinction
Experiment Description	We aim to understand 1) how the spatial gene expression pattern in medial prefrontal cortex changes after fear extinction, and 2) if each projection-specific population of prefrontal cortex has unique gene expression after the extinction.
Experimental Design	sex design	stimulus or stress design
Experimental Factor Name	extinction
Experimental Factor Type	extinction
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	2025-05-21
Protocol Name	P-GEAD-845	P-GEAD-846	P-GEAD-847	P-GEAD-848	P-GEAD-849
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	The brains were collected after cervical dislocation, immediately frozen in liquid nitrogen, and stored at -80 until the sectioning. Following the Visium protocol, cryostat sectionings were put on the Visium slide, fixed by methanol, and stained with DAPI.	Visium Spatial Gene Expression Reagent Kits(10x Genomics)	Visium Spatial Gene Expression Reagent Kits(10x Genomics)	Paired-end sequencing was performed by Illumina NovaSeq6000; 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; M1_HC_F1_HC:slide=V10U22-102,area=A1,M3_Ext_F2_Ext:slide=V10U22-102,area=B1,M4_HC_F4_HC:slide=V10U22-102,area=C1,M6_Ext_F5_Ext:slide=V10U22-102,area=D1
SDRF File	E-GEAD-434.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB11713
Comment[Last Update Date]	2025-05-21