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Sample GSM6735425 Query DataSets for GSM6735425
Status Public on May 14, 2024
Title ChIP-seq_H3K27ac_CD4T_control
Sample type SRA
 
Source name Lung
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: WT
tissue: Lung
cell type: CD4 T cells
condition: control
chip antibody: H3K27ac (abcam, ab4729)
Treatment protocol Mice were administered with 10 µg of HDM at day -6 and day 0-4. Cells were harvested at day 0 for control and day 6 for asthma.
Extracted molecule genomic DNA
Extraction protocol Lungs were cut into small pieces and digested in RPMI containing collagenase A and Dnase I using gentleMACS Dissociator and then passed through 70 µm filter. Lung ILC2s and CD4 T cells were sorted by SONY SH800 following crosslink with 1% formaldehyde.
Sonicated samples were immunoprecipitated using H3K27ac antibody (ab4729, Abcam) and Dynabeads Protein A. Chromatin-DNA complexes were washed seven times and reverse-croslinked by overnight incubation at 65 ˚C. DNA fragments were harvested with phenol-chloroform extraction followed by ethanol precipitation. ChIP-seq libraries were prepared with ThruPLEX DNA-seq kit.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing ChIP-seq data were aligned to mm10 genome assembly using Bowtie2 with single-end mode. The data were visualized and the SEs were identified using the HOMER package.
Assembly: mm10
Supplementary files format and content: bedgraph
 
Submission date Nov 16, 2022
Last update date May 14, 2024
Contact name Arifumi Iwata
Organization name Chiba University
Department Department of Allergy and Clinical Immunology
Street address 1-8-1 Inohana, Chuou-ku
City Chiba-shi
State/province Chiba
ZIP/Postal code 260-8670
Country Japan
 
Platform ID GPL17021
Series (2)
GSE218144 H3K27ac ChIP-seq for lung ILC2 and CD4 T cells in HDM induced asthma
GSE218155 ILC2 development requires GATA3-related super-enhancers after lineage commitment
Relations
BioSample SAMN31760265
SRA SRX18289073

Supplementary file Size Download File type/resource
GSM6735425_ChIP-seq_H3K27ac_CD4T_control.bedgraph.gz 118.3 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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