|
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 |