|
| Status |
Public on May 01, 2024 |
| Title |
HiC_NK_WT |
| Sample type |
SRA |
| |
|
| Source name |
NK cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
cell type: NK cells
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.
|
| Growth protocol |
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.
|
| Extracted molecule |
genomic DNA |
| 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.
3-5 million cells were aliquoted from pooled naïve T cells or Th1 cells differentiated in vitro for each genotype, then pelleted and fixed with formaldehyde (1% v/v) for 5 minutes with mixing, before the reaction was quenched with glycine (0.2M). Cells were washed, pelleted, and flash frozen on dry ice for storage in -80°C before the Hi-C protocol was initiated. Global Hi-C was performed according to previously published protocols (Rao, 2014). After global Hi-C was completed, 500 ng of Hi-C libraries were used as the pond for the hybrid selection reaction. A 1,550,000 bp region surrounding the Ifng locus was hybridized using a collection of 2367 RNA probes. Local in situ Hi-C was performed according to previously published protocols.
DNA libraries were constructed according to to previously published protocols.
DNA libraries were sequenced at 100 million reads with 50bp paired-end reads using NovaSeq (Illumina).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
alignment: Hi-C sequencing reads from two biological replicates for each cell type and genotype were trimmed using HOMER, then mapped to the mouse genome (mm10) using Bowtie.
peaks: Hi-C tag directories were created using HOMER. And Hi-C interaction matrices were generated and normalized using HOMER with parameters -res 1000 -window 5000 -balance -corr. The interaction matrices were converted to .h5 files and visualized using HiCExplorer after merging the two biological replicates.
Supplementary files format and content: text or .h5 or .hic files for focuesed Hi-C.
|
| |
|
| Submission date |
Jun 30, 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) |
| GSE215178 |
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 |
SAMN36185783 |
| SRA |
SRX20860792 |
