Comment[GEAAccession]	E-GEAD-609
MAGE-TAB Version	1.1
Investigation Title	scRNA-seq of splenic macrophage re-clustering about cholinergic anti-inflammatory pathway
Experiment Description	Wild-type mice (8 weeks old, C57BL6J male mice, 20-23g) were injected intraperitoneally LPS (5mg/kg) and GTS-21(20 mg/kg) or Normal saline (Ns). Then they euthanized 4 hrs later. After spleens were harvested, digested with digestion buffer, and obtained single-cell suspensions. Macrophages in the spleen were extracted using a magnetic cell sorting system (MACS). Then 7000 cells from each samples were used single-cell RNA-seq. This is the splenic macrophage-enriched sample. The splenic macrophage sample consists of two samples, LPS_Ns and LPS_GTS. The dataset2 is the analyzed data of splenic macrophages sample, which containing immune cells (e.g. B cells and T cells) other than macrophages. The dataset 3 is the analyzed data extracted and analyzed from dataset 2 only for the labels that were predicted to be macrophages.
Experimental Design	injury design
Experimental Factor Name	treatment
Experimental Factor Type	treatment
Person Last Name	Nakamura	Inoue	Matsumoto
Person First Name	Yasuna	Tsuyoshi	Hirotaka
Person Affiliation	Nagasaki University		
Person Roles	submitter	submitter	submitter
Public Release Date	2024-07-29
Protocol Name	P-GEAD-1792	P-GEAD-1793	P-GEAD-1794	P-GEAD-1795	P-GEAD-1796
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Wild-type (C57BL6J, 8 weeks old, male) mice treated with GTS-21with or without LPS four hours, then euthanized and harvested spleens. Splenic macrophages were obtained using magnetic cell sorting system.	Seven thousand cells were loaded onto a 10x Genomics Chromium Instrument to create single-cell Gel Beads.	cDNA libraries were constructed using 10x Chromium Single Cell 3' Reagent Kits v3.1(10x Genomics), following the manufacturers instructions.	The quality of the libraries was checked using an Agilent 2200 Tapestation System, then libraries were sequenced using Illimina NovaSeq 6000 platform.	The fastq files were processed using Cell Ranger v3.1.0. count pipeline against the mm10 (v3.0.0) mouse reference sequence. The data was normalized using the \"NormalizeData\" function.
SDRF File	E-GEAD-609.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA from single cells
Comment[BioProject]	PRJDB14097
Comment[Last Update Date]	2024-07-29