|
| Status |
Public on Sep 30, 2022 |
| Title |
4: A549 SARS-CoV-2 ORF3-2 |
| Sample type |
SRA |
| |
|
| Source name |
SARS-CoV-2 ORF3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
transfection: SARS-CoV-2 ORF3
|
| Treatment protocol |
A549 cells were transfected with empty vector or Flag-ORF3,36h post transfection, cells were collected(two separate experiments)
|
| Growth protocol |
A549 cells were cultured in 1640 medium (with 10% serum)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Medium were removed, and RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Qualified libraries were sequenced using Illumina platform. The sequencing strategy was PE150.
Raw Reads were obtained from Illumina sequencing. Clean Reads were obtained through data processing such as removal of low-quality sequences and joint contamination. All subsequent analyses were based on Clean Reads.
FPKM (Trapnell, C. et al., 2010) is a very effective tool to quantitatively estimate gene expression values using RNA-seq technology. FPKM is an abbreviation for Fragments per Kilobase per Million Fragments, the number of Fragments per thousand bases that are derived from a specific gene. It is the most commonly used gene expression level estimation method that takes into account the sequencing depth and gene length effect on the count of Fragments.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Sep 24, 2020 |
| Last update date |
Sep 30, 2022 |
| Contact name |
Xiaolin Zhang |
| E-mail(s) |
zhangxlin7@mail2.sysu.edu.cn, 1933246727@qq.com
|
| Organization name |
Sun Yat-sen University
|
| Street address |
No.74 Zhongshan 2nd Road
|
| City |
Guangzhou |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE158484 |
Functions of SARS-CoV-2 ORF3 during Virus Infection |
|
| Relations |
| BioSample |
SAMN16253312 |
| SRA |
SRX9183005 |
