Comment[GEAAccession]	E-GEAD-450
MAGE-TAB Version	1.1
Investigation Title	Rat renal cell atlas and perturbation by losartan characterized with single-cell and spatial transcriptome information
Experiment Description	To identify the local changes of the gene expression patterns by administration of losartan at single cell level, we performed both single cell RNA sequencing (scRNA-seq) and spatial transcriptome sequencing (ST-seq) of the kidney from the rat treated with or without losartan. The sequencing library for scRNA-seq were prepared by Chromium Single Cell 3 Library Kit v2 (10x Genomics) and that for ST-seq were prepared by Visium Spatial Gene Expression Slide & Reagents Kit (10x Genomics). Following the integration analysis of scRNA-seq and ST-seq, we detected the spatially restricted changes of the gene expression patterns by administration of losartan in several cell types, such as macula densa cells or juxtaglomerular cells. We further analyze the ST-seq data in combination with the deconvolution tool, using scRNA-seq as a reference, and consequently observed spatial heterogeneity in the response to losartan among the glomeruli.
Experimental Design	compound treatment design
Experimental Factor Name	Drug intervention
Experimental Factor Type	Drug intervention
Person Last Name	Onoda	Onoda	Kawabata	Sakakura	Urakawa	Seki	Suzuki	Suzuki	Sequence
Person First Name	Naoki	Naoki	Ayako	Megumi	Itaru	Masahide	Ayako	Yutaka	Kashiwa
Person Affiliation	Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo								
Person Roles	submitter	submitter	submitter	submitter	submitter	submitter	submitter	submitter	submitter
Public Release Date	2021-12-10
Protocol Name	P-GEAD-928	P-GEAD-929	P-GEAD-930	P-GEAD-931	P-GEAD-932
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 kidneys from the rats were horizontally divided into 3 pieces and each central part was further divided into 2 pieces. Each piece of kidney was embedded into OCT (Sakura Finetek Japan; 4583) and immediately fresh frozen on dry ice. Frozen tissue sections of 10 um thickness were sliced (Leica CM1950) and affixed to the slides for spatial sequencing.	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; Ctrl1:slide=V10A14-156,area=A1, Ctrl2:slide=V10A27-117,area=C1, Ctrl3:slide=V10A27-117,area=D1, Losa1:slide=V10A14-156,area=B1, Losa2:slide=V10A14-156,area=C1, Losa3:slide=V10A14-156,area=D1
SDRF File	E-GEAD-450.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB12203
Comment[Last Update Date]	2021-12-10