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| Status |
Public on May 02, 2024 |
| Title |
PAX-1_48h |
| Sample type |
SRA |
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| Source name |
293T cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: 293T cells
cell type: human embryonic kidney
treatment: parental PAX
time: 48h
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| Treatment protocol |
To evaluate the role of specific amino acids of PA-X in inhibiting host protein expression, 293T cells (24-well plate, 2×105.0 cells/well, in triplicate) were transfected with 50 ng/well of pCDNA-3.1 encoding PA-X proteins from the parental GD15 virus (PAX) or the mutant PA-X protein or the PCAGGS empty vector as an internal control. and then stored at -80 ℃ for further RNA-seq.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using miRNeasy Mini Kit (Qiagen, USA) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit
Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 4200 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration.
Tophat v2.1.0 were used to map the cleaned reads to the human h38 reference genome with two mismatches. After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models. Significant differentially expressed (SDE) genes were identified using Cuffdiff.
The p-value significance threshold in multiple tests was set by the false discovery rate (FDR)
Assembly: human h38 reference genome
Supplementary files format and content: tab-delimited text files include coutn and FPKM values for each sample.
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| Submission date |
May 25, 2022 |
| Last update date |
May 02, 2024 |
| Contact name |
Jiao Hu |
| E-mail(s) |
hujiao@yzu.edu.cn
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| Organization name |
Yangzhou University
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| Street address |
48 Wenhui Road
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| City |
Yangzhou |
| ZIP/Postal code |
225009 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE204790 |
RNA-seq data of 293T cells trasfected with different viral PA-X proteins of influenza viruses |
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| Relations |
| BioSample |
SAMN28657296 |
| SRA |
SRX15450758 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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