|
| Status |
Public on Aug 16, 2023 |
| Title |
TrainedBasalRep2 |
| Sample type |
SRA |
| |
|
| Source name |
Lung macrophage
|
| Organism |
Mus musculus |
| Characteristics |
group: 7day-LPS-trained
cell type: Lung macrophage
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The flow sorted alveolar macrophages were collected. 200,000 cells were then further used for ATACseq using Active Motif Kit Cat # 53150 by following the manufraturer protocol
Library were contructed with 10 cycles of PCR using the Active motif Kit Cat # 53150, index promer according to the manufracturer protocol
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
countsFromATAC.csv
|
| Data processing |
Adapters were trimmed by TrimGalore.
Trimmed reads were aligned to the mm10 reference genome using Bowtie2.
Unique reads with a quality score equal or more than 30 were kept. Tn5 offset was asjusted.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Irreproducibility Discovery Rate framework was applied to get peaks that were consistent among biological replicates.
Count tables were generated using Rsubread R package.
Assembly: mm10
Supplementary files format and content: narrowPeak, csv
|
| |
|
| Submission date |
Apr 28, 2023 |
| Last update date |
Aug 16, 2023 |
| Contact name |
Jalees Rehman |
| E-mail(s) |
jalees@uic.edu
|
| Organization name |
UIC
|
| Department |
Biochemistry and Molecular Genetics
|
| Street address |
909 S. Ashland Ave. MBRB 2072, Mailcode 669
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60607 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE231217 |
Trained immunity of alveolar macrophages promotes injury resolution by enhancing KLF4-MERTK-mediated efferocytosis |
| GSE231219 |
Trained immunity of alveolar macrophages promotes injury resolution by enhancing KLF4-MERTK-mediated efferocytosis. |
|
| Relations |
| BioSample |
SAMN34432313 |
| SRA |
SRX20141794 |
