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| Status |
Public on May 01, 2024 |
| Title |
ATAC_Th1_d3_KO_1 |
| Sample type |
SRA |
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| Source name |
Th1 cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
culture condition: ex vivo
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| 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.
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| 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.
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| 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).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Aug 30, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Vijay Nagarajan |
| Organization name |
National Institutes Of Health
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| Department |
National Eye Institute
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| Lab |
Laboratory of Immunology
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| Street address |
10 Center Drive, 10/10N248
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| 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] |
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| Relations |
| BioSample |
SAMN37205084 |
| SRA |
SRX21541792 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7747462_ATAC_Th1_d3_KO_1_mm10.bw |
322.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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