|
| Status |
Public on May 01, 2024 |
| Title |
bulkRNA_Th1_D3_WT2 |
| 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
LCMV 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).
cDNA libraries were sequenced at 20 million reads per sample with 50bp paired-end reads using NovaSeq or NextSeq (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
bulkRNA_Th1_D3_anti-gamma_IFNg_results.gene.rpkm.xlsx
bulkRNA_Th1_D3_anti-gamma_IFNg_results.gene.ANOVA.xlsx
|
| Data processing |
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 |
Jun 29, 2023 |
| 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 |
|
| Relations |
| BioSample |
SAMN36084344 |
| SRA |
SRX20833004 |
