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Sample GSM6625288 Query DataSets for GSM6625288
Status Public on May 01, 2024
Title scRNA_KO_Spleen_NK_Toxo_day3
Sample type SRA
 
Source name NK cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
cell type: NK cells
culture condition: in vivo
Treatment protocol Toxoplasma gondii infection protocol: Wild type and IfngCTCFdel mice were inoculated with an average of 15 cysts of type II avirulent T. gondii strain ME-49 by intraperitoneal injection
Toxoplasma gondii infection protocol: LCMV (strain Armstrong) was thawed at 37°C and then injected into mice by intraperitoneal injection at the concentration 2 x 10^5 plaque-forming units (PFU) per mouse.
Extracted molecule total RNA
Extraction protocol cell isolation protocol: Cells from spleen were obtained by mechanical disruption. Peritoneal cells were obtained by washing of the peritoneal cavity with cold PBS. Isolated cells were further sorted as based on their surface markers.
in vitro culture protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10 ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.
Single cell suspensions were sorted using a FACS Aria Fusion (BD). ~15K cells at a concentration of 800 cells/μl were processed using the Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, #1000121), the Chromium Next GEM Chip G Single Cell Kit (10x Genomics, #1000120) and the Chromium Controller (10x Genomics, #1000202). cDNA libraries were constructed using the Chromium Single Cell 3ʹ Library Kit (10x Genomics, #1000079) and Single Index Kit T Set A (10x Genomics, #1000213).
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing cDNA libraries were sequenced at ~500 million reads per sample with 50bp paired-end reads using NovaSeq (Illumina).
alignment: Sequencing reads were processed using Cell Ranger 3.0 (10x Genomics) to generate the FastQ files and cell counts. The matrix files generated from Cell Ranger were further analyzed using Seurat including quality control, filtering, normalization, scaling, clustering, visualization, differential expression analysis, cell population annotation. Gene Ontology (GO) analysis were performed using Enrichr and ggplot2 (https://ggplot2.tidyverse.org) in R. Downstream analyses were performed with custom R programs (http://www.R-project.org/).
Assembly: mm10
Supplementary files format and content: .h5 files for single cell RNA-seq
 
Submission date Oct 10, 2022
Last update date May 01, 2024
Contact name Vijay Nagarajan
Organization name National Institutes Of Health
Department National Eye Institute
Lab Laboratory of Immunology
Street address 10 Center Drive, 10/10N248
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
Platform ID GPL24247
Series (2)
GSE215180 Selective requirement of 3D genomic organization for the Mdm1-Il22-Ifng locus regulation in initial Th1 cell lineage specification and differentiation
GSE215181 Selective requirement of 3D genomic organization for the Mdm1-Il22-Ifng locus regulation in initial Th1 cell lineage specification and differentiation
Relations
BioSample SAMN31231268
SRA SRX17843012

Supplementary file Size Download File type/resource
GSM6625288_scRNA_KO_Spleen_NK_Toxo_day3.h5 8.7 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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