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Sample GSM6625193 Query DataSets for GSM6625193
Status Public on May 01, 2024
Title naïve_CD4_D0_K27Ac_141007_0175_s9
Sample type SRA
Source name Naïve T cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
cell type: naive T cells
culture condition: ex vivo
chip antibody: anti-H3K27ac
chip antibody vendor: Abcam
chip antibody cat.#: ab4729
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.
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).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model NextSeq 550
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
Submission date Oct 10, 2022
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 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
BioSample SAMN31231202
SRA SRX17842913

Supplementary file Size Download File type/resource 233.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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