|
| Status |
Public on Jan 25, 2024 |
| Title |
ATACseq_Mac_30min_4 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell line: Hoxb8
cell type: Macrophages
treatment: +Apoptotic Jurkat cells (30min)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 viable cells were resuspended in cold Lysis Buffer. Cells were resuspended in transposition mix containing TD buffer and Tn5 transposase.DNA purification was performed using Quagen MinElute Reaction Cleanup kit.
A modified version of the Omni-ATAC-seq protocol was used to preparae libraries (PMID: 28846090). Adapter ligation and amplification were carried out using Nextera Index Kit (Illumina).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Trimmomatic v0.36 to cut NexteraPE adapter sequences. Bowtie v2.3.5 was used to align pair-end ATAC-seq read to the mm10 mouse reference genome. Bedtools package v2.30.089 was used to compute the consensus peak set for each condition.
Assembly: mm10
Supplementary files format and content: bw: BigWig genome browser track for ATAC-seq data
|
| |
|
| Submission date |
Jan 18, 2024 |
| Last update date |
Mar 18, 2024 |
| Contact name |
Kodi S Ravichandran |
| E-mail(s) |
kodi@wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Department |
Pathology and Immunology
|
| Street address |
660 Euclid Ave
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63108 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE253574 |
Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release (ATAC-Seq) |
| GSE253578 |
Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release |
|
| Relations |
| BioSample |
SAMN39489261 |
| SRA |
SRX23306999 |
