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Sample GSM5135062 Query DataSets for GSM5135062
Status Public on Sep 22, 2021
Title Spleen-WT_scRNA-seq
Sample type SRA
Source name Spleen
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
age: post natal week 6
genotype: NKp46iCre+
Extracted molecule total RNA
Extraction protocol Mononuclear cells are isolated from the spleen following red blood cell lysis. NK cells are enriched by Magnetic Cell Sorting (Miltenyi) for library construction.
The 10x Genomics Chromium single-cell 3’ v4 kit and protocol was used to prepare the library.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Raw FASTQ files were processed with Cell Ranger software (v1.3.1) for alignment, filtering, barcode counting and UMI counting.
Further analysis was performed with Seurat, by selecting highly variable genes using FindVariableGenes functions with default parameters, reduced the dimensionality by PCA, and clustered the cells using FindNeighbors and FindClusters.
We applied RunUMAP for visualization.
For comparison of splenic NK cells from NK-specific TIPE2 deficient mice or control mice, the data including 4270 NK cells from NK-specific TIPE2 deficient mice, and 4488 NK cells from control mice were merged for analysis.
Genome_build: mm10
Supplementary_files_format_and_content: processed seurat object files
Submission date Mar 04, 2021
Last update date Sep 22, 2021
Contact name Jiacheng Bi
Organization name Shenzhen Institute of Advanced Technology
Street address 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, P.R.China
City Shenzhen
ZIP/Postal code 518055
Country China
Platform ID GPL24247
Series (1)
GSE168256 TIPE2 is a checkpoint in natural killer cell maturation and anti-tumor immunity
BioSample SAMN18140423
SRA SRX10239441

Supplementary file Size Download File type/resource
GSM5135062_processed_seurat_object-WT.rds.gz 571.8 Mb (ftp)(http) RDS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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