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Sample GSM6625278 Query DataSets for GSM6625278
Status Public on May 01, 2024
Title bulkRNA_Th1_D7_Ifng(70)CTCFdel_F_WT3
Sample type SRA
Source name Th1 cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
cell type: th1
culture condition: ex 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 polyA 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.
Total RNA was extracted from 200,000 cells using QIAzol Lysis Reagent and the Direct-zol microprep RNA kit.
mRNA purification, cDNA synthesis and cDNA library preparation was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, #E7770) and NEBNext Multiplex Oligos for Illumina (NEB, #E6609).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing cDNA libraries were sequenced at 20 million reads per sample with 50bp paired-end reads using NovaSeq or NextSeq (Illumina).
alignment: The run was demultiplexed and converted to FastQ using bcl2fastq v2.20.0.422 (Illumina) and mapped to mm10 using Tophat 2.1.0.
FPKM: Partek Genomics Suite 7.0 (Partek) was used to calculate Reads Per Kilobase of transcript, per Million mapped reads (RPKM), perform analysis of variance (ANOVA) comparisons, perform principal component analysis (PCA) and perform hierarchical clustering.
Assembly: mm10
Supplementary files format and content: excel files for bulk 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)
GSE215179 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
BioSample SAMN31231206
SRA SRX17842895

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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