|
| Status |
Public on May 28, 2023 |
| Title |
Mouse Alveolar Macrophage, 2 months post vaccinated with dNS1-Vector 1 |
| Sample type |
SRA |
| |
|
| Source name |
Alveolar Macrophage
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Alveolar Macrophage
treatment: Vaccinated with dNS1-Vector
|
| Treatment protocol |
C57BL/6v mice lungs were collected 2 months post-vaccination and sorted for bronchoalveolar lavage AMs using a BD FACS Aria Fusion machine. One hundred thousand sorted cells were centrifuged at 500 × g for 10 min at 4 °C per replicate.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed with lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM MgCl2, and 0.1% IGEPAL CA-630). Libraries were prepared using the TruePrep DNA library prep kit V2 for Illumina (Vazyme) according to the manufacturer’s instructions.
Libraries were cleaned up with AMPure XP beads (Beckman coulter) at a ratio of 0.7 and the quality was assessed using the 2100 Bioanalyzer (Agilent Technologies). Libraries were sequenced with 150 paired ends using a NovaSeq 6000 instrument (Illumina) for an average of 20 million reads per sample.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
B_AM_1
|
| Data processing |
Sequence reads were trimmed and adaptor removed by using fastp.
Cleanned sequence reads were mapped to mm10 mouse genome by using bowtie2
The duplicated and low-quality fragments were removed by using picard and samtools
To create ATAC-seq coverage plots, the locations of the mapped ATAC-seq reads were extended to 150 bp to represent sequenced fragments, renormalized and reformatted in the bigWig file format.
Peaks were called uing MACS2 with the significance cut-off q-value <=0.01, narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
|
| |
|
| Submission date |
Mar 19, 2023 |
| Last update date |
May 28, 2023 |
| Contact name |
Jinhang He |
| E-mail(s) |
hejinhang@stu.xmu.edu.cn
|
| Phone |
15821251893
|
| Organization name |
Xiamen University
|
| Street address |
No.4221, South Xiang'an Road
|
| City |
Xiamen |
| State/province |
Fujian |
| ZIP/Postal code |
361104 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE227648 |
Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response (Mouse AMs ATAC-seq Data) |
| GSE227649 |
Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response |
|
| Relations |
| BioSample |
SAMN33818996 |
| SRA |
SRX19719244 |
