|
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)
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|
|
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 |