|
| Status |
Public on May 28, 2023 |
| Title |
7 day post Influenza CA04 infected, replicate 1, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Lung Tissue
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Lung Tissue
tissue: Lung Tissue
strain: C57BL/6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions with 1×105 cells/mL in concentration in PBS were prepared. Single-cell suspensions were loaded into microfluidic devices and scRNA-seq libraries were constructed following the Singleron GEXSCOPER protocol by GEXSCOPER Single-Cell RNA Library Kit (Singleron Biotechnologies).
Indivaidual libraries of each sample were then dilyted to 4nM, pooled and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Singleron Matrix GEXSCOPE
|
| Data processing |
The demultiplexing, barcoded processing, alignment, gene counting and aggregation were made using the Singleron Celescope software version 1.10.0 (https://github.com/singleron-RD/CeleScope)
The doublet were removed by using Doubletfinder R package and personal checking for conserved markers.
The R package Seurat version 4.1.1 was used for normalization, clustering and reduction. Cell type was annotated based on conserved markers.
Differential gene expression analysis and enrichment analysis were performed by using MAST and clusterProfiler R package.
Assembly: GRCm38
Supplementary files format and content: Compressed .tar.gz file containing genes, barcodes and matrix for each sample
|
| |
|
| Submission date |
Mar 30, 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) |
| GSE227649 |
Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response |
| GSE228594 |
Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response (Mouse Lung scRNA-seq Data) |
|
| Relations |
| BioSample |
SAMN33994882 |
| SRA |
SRX19832295 |
