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Sample GSM7747463 Query DataSets for GSM7747463
Status Public on May 01, 2024
Title ATAC_Th1_d3_KO_2
Sample type SRA
 
Source name Th1 cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
culture condition: ex vivo
Treatment 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 (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 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 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.
FastATAC-Seq was performed according to a published protocol(Corces et al., 2016) 10,000 sorted cells were pelleted and washed with 50 μl 1x PBS. After pelleting the nuclei by centrifuging at 500 x g for 10 minutes at 4°C, the pellets were re-suspended in 50 μl transposase mixture (25 μl of 2x TD buffer, 2.5 μl of TDE1, 0.5 μl of 1% digitonin, 22 μl of nuclease-free water) (Illumina, #20034197 and Promega, #G9441) to tag and fragmentalize accessible chromatin. The reaction was incubated at 37°C with shaking at 300 rpm for 30 minutes. The fragmentalized DNAs were then purified using a QIAGEN MinElute kit (Qiagen, #28006) and amplified with appropriate cycles of PCR based on the amplification curve using NEBNext High-Fidelity 2x PCR Master Mix (NEB, #M0541) and SYBR Green I (Thermo Fisher Scientific, #S-7563).
Once the libraries were purified using a QIAGEN PCR cleanup kit (Qiagen, #28106), they were further sequenced for 50bp paired-end reads on NovaSeq or NextSeq (Illumina).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing ATAC-seq reads from two biological replicates were mapped to the mouse genome (mm10 assembly) using Bowtie 45. Redundant reads were removed using FastUniq 46.
Customized Python scripts were used to calculate the fragment length of each pair of uniquely mapped paired-end (PE) reads. BigWig tracks were generated by HOMER 20 and visualized by IGV genome browser 47.
Assembly: mm10
Supplementary files format and content: bigwig files for ATAC-seq
 
Submission date Aug 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)
GSE215181 Selective requirement of 3D genomic organization for the Mdm1-Il22-Ifng locus regulation in initial Th1 cell lineage specification and differentiation
GSE242000 Selective requirement of 3D genomic organization for the Mdm1-Il22-Ifng locus regulation in initial Th1 cell lineage specification and differentiation [ATAC-Seq]
Relations
BioSample SAMN37205083
SRA SRX21541793

Supplementary file Size Download File type/resource
GSM7747463_ATAC_Th1_d3_KO_2_mm10.bw 75.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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