|
| Status |
Public on Jun 30, 2020 |
| Title |
HMGB1 challenge Donor 2-1 |
| Sample type |
SRA |
| |
|
| Source name |
Healthy primary neutrophils challenged with HMGB1 for 1 hour
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: neutrophils
|
| Treatment protocol |
Neutrophils from healthy female voulnteers betewen 31-40 were challenged with 6 pathogen mimicking ligands and whole blood from vounteers were challenged with 2 whole organisms.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed as previously published and excess primers were removed using AMPpure bead kit.
Libraries generated using KAPA PolyA enrichment mRNA library prep
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
ATAC-seq peak calling was done using PEPATAC by including all Donor and Replicate fastqs for each challenge and control
Genome_build: hg19
Supplementary_files_format_and_content: Peaks called from Donor and Replicate merged fastqs, includes coverages
|
| |
|
| Submission date |
Jun 29, 2020 |
| Last update date |
Jun 30, 2020 |
| Contact name |
Samuel Yang |
| Organization name |
Stanford University School of Medicine
|
| Department |
Emergency Medicine
|
| Street address |
1201 Welch Road
|
| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE153520 |
Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection [ATAC-seq] |
| GSE153522 |
Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection |
|
| Relations |
| BioSample |
SAMN15087020 |
| SRA |
SRX8456500 |
