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| Status |
Public on May 01, 2024 |
| Title |
scRNA_KO_Spleen_Th1_Toxo_day3 |
| Sample type |
SRA |
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| Source name |
Th1 cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
cell type: Th1 cells
culture condition: in vivo
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| 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.
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Oct 10, 2022 |
| Last update date |
May 01, 2024 |
| Contact name |
Vijay Nagarajan |
| Organization name |
National Institutes Of Health
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| Department |
National Eye Institute
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| Lab |
Laboratory of Immunology
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| Street address |
10 Center Drive, 10/10N248
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN31231267 |
| SRA |
SRX17843013 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6625289_scRNA_KO_Spleen_Th1_Toxo_day3.h5 |
8.1 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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