|
| Status |
Public on May 14, 2024 |
| Title |
ATAC-seq_G3SEKO_BM3_IL18Ra+ST2-PD1-IL17RB+ |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
genotype: G3SEKO
treatment: no treatment
|
| 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 were sorted by SONY SH800. Bone marrow cells were harvested and lineage-positive cells were depleted using MojoSort Mouse Hematopoietic Progenitor Cell Isolation Kit. Each fraction of ILC2 lineages were sorted by BD Melody.
ATAC-seq library was generated using Omni-ATAC protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ATAC-seq data were aligned to mm10 genome assembly using Bowtie2 with paired-end mode. Mapped fragments were trimmed 4 bp from the start and 5 bp from the end using bedtools. The data were visualized and the peaks were identified using the HOMER package.
Assembly: mm10
Supplementary files format and content: bedgraph
|
| |
|
| Submission date |
Mar 15, 2024 |
| 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 |
GPL19057 |
| Series (2) |
| GSE218142 |
ATAC-seq of bone marrow ILC2 lineages and Lung ILC2 steady state |
| GSE218155 |
ILC2 development requires GATA3-related super-enhancers after lineage commitment |
|
| Relations |
| BioSample |
SAMN40474076 |
| SRA |
SRX23963031 |
