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| Status |
Public on May 01, 2024 |
| Title |
ChIP_Th1_D3_H3K27ac_F_WT1 |
| Sample type |
SRA |
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| Source name |
Th1 cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
cell type: Th1 cells
culture condition: ex vivo
chip antibody: anti-H3K27ac
chip antibody vendor: Abcam
chip antibody cat.#: ab4729
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| 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.
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| 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.
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.
ChIP was performed for transcription factors CTCF (Millipore Sigma, #07-729), Rad21 (Abcam, #ab992) and p300 (Abcam, #ab14984) using SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology, #9005S). ChIP was performed for histone marks H3K27ac (Abcam, #ab4729), H3K27me3 (Thermo Fisher Scientific, #MA511198) and H3K4me1 (Abcam, #ab8895) using iDeal ChIP-seq Kit for Histones (Diagenode, #C01010051).
The purified enriched DNA was used to generate libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645) and NEBNext Multiplex Oligos for Illumina (NEB, #E6609).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
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| Data processing |
DNA libraries were sequenced at 20 million reads per sample with 50bp paired-end reads using NovaSeq or NextSeq (Illumina).
alignment: Sequencing data from ChIP-Seq were mapped onto mouse genome build mm10 using Bowtie 0.12.8 (reference #46). BigWig tracks were generated by the Hypergeometric Optimization of Motif EnRichment program (HOMER) (Reference #45) and visualized by IGV (Nature Biotechnology 29, 24–26 (2011)).
peaks: MACS (version 1.4.2) (Genome Biology volume 9, Article number: R137 (2008)) was used for peak calling of transcription factor ChIP-Seq using a P-value threshold of 1 x 10-5. Downstream analyses and graph generation were performed with HOMER and R.
Assembly: mm10
Supplementary files format and content: bigwig files for ChIP-seq
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| Submission date |
Oct 10, 2022 |
| 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 |
GPL21626 |
| Series (2) |
| GSE215177 |
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 |
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| Relations |
| BioSample |
SAMN31231153 |
| SRA |
SRX17842946 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6625242_ChIP_Th1_D3_H3K27ac_F_WT1.bw |
201.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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