Comment[GEAAccession]	E-GEAD-462
MAGE-TAB Version	1.1
Investigation Title	Semibulk RNA-seq analysis as a convenient method for measuring gene expression statuses in a local cellular environment
Experiment Description	Murine kidney was harvested from a mouse and snap frozen by spray freezing with OCT compounds. A 10-µm cryosection was prepared by cryostat and put on the Visium Spatial Gene Expression Slide (Visium Spatial Gene Expression Slide Kit, 10x Genomics). Fixation and H&E staining were conducted according to the Tissue Fixation & Staining Demonstrated Protocols provided from 10x Genomics. H&E visualization was conducted using BZ-X800 (KEYENCE). Tissue permeabilization, cDNA amplification and library preparation were performed using Visium Spatial Gene Expression Reagent Kits according to the manufacturer's protocol. For tissue permeabilizaion, incubation time was set to 18 minutes. Sequencing was performed using Illumina NovaSeq 6000.
Experimental Design	cell component comparison design
Experimental Factor Name	LIBRARY_TYPE
Experimental Factor Type	LIBRARY_TYPE
Person Last Name	Suzuki	Seki	Sequence
Person First Name	Yutaka	Masahide	Kashiwa
Person Affiliation	Suzuki Lab  Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences, The University of Tokyo		
Person Roles	submitter	submitter	submitter
Public Release Date	2022-08-23
Protocol Name	P-GEAD-994	P-GEAD-995	P-GEAD-996	P-GEAD-997	P-GEAD-998
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	A female mouse of ICR strain  at the age of 10 weeks was purchased from Japan ICR.	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(10x Genomics).  Slide information;slide=V10Y04-066,area=A1
SDRF File	E-GEAD-462.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB12548
Comment[Last Update Date]	2022-08-23