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Sample GSM7527915 Query DataSets for GSM7527915
Status Public on May 01, 2024
Title Focused-HiC_Th1_D3_F_KO2
Sample type SRA
Source name Th1 cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
cell type: Th1 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
BioSample SAMN36185784
SRA SRX20860791

Supplementary file Size Download File type/resource
GSM7527915_Focused-HiC_Th1_D3_F_KO2.mm10.hic 1.2 Gb (ftp)(http) HIC
GSM7527915_Focused-HiC_Th1_D3_F_KO2.res1K.win15K.balance.corr.mm10.h5 652.7 Kb (ftp)(http) H5
GSM7527915_Focused-HiC_Th1_D3_F_KO2.res1K.win15K.balance.corr.mm10.txt.gz 442.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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