|
| 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 |
