|
| Status |
Public on Dec 31, 2020 |
| Title |
ΔCSP1 |
| Sample type |
SRA |
| |
|
| Source name |
HepG2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
genotype: overexpressing {delta}CSP
|
| Growth protocol |
HepG2 cells were infected with overexpression ΔCSP and control lentivirus for 48h, then the ΔCSP stably transfected and control cells were screened by 5mg/mL puromycin (Gibco) and sorted by flow cytometry, finally cloned by limited dilution method continually in 96-well and 3mg/mL puromycin was used to maintain the resistance of stable transfected cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs of ΔCSP stable expressing or control HepG2 cells were extracted using TRIzol (Invitrogen), following the manufacturer's instructions.
Sequencing libraries were generated using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Vazyme Biotech, Nanjing, China) following manufacturer's recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
ΔCSP stable expressing HepG2 cells
|
| Data processing |
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis.
Clean reads were mapped to the reference genome by HISAT2 (version 2.0) with default parameters. RSeQC (version 2.6.1) was used to statistics the alignment results. The homogeneity distribution and the genome structure were checked by Qualimap (version 2.2.1). BEDTools (version 2.26.0) was used to statistical analysis the gene coverage ratio.
Gene expression values of the transcripts were computed by StringTie (version 1.3.3b). Principal Component Analysis (PCA) and Principal co-ordinates analysis (PCoA) were performed to reflect the distance and difference between samples. The TPM (Transcripts Per Million), eliminates the influence of gene lengths and sequencing discrepancies to enable direct comparison of gene expression between samples. DESeq2 (version 1.12.4) was used to determine differentially expressed genes (DEGs) between two samples. Genes were considered as significant differentially expressed if q-value <0.001 and |FoldChange| >2. When the normalized expression of a gene was zero between two samples, its expression value was adjusted to 0.01 (as 0 cannot be plotted on a log plot). If the normalized expression of a certain gene in two libraries was all lower than 1, further differential expression analysis was conducted without this gene. Gene expression differences were visualized by scatter plot, MA plot and volcano plot.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample …
|
| |
|
| Submission date |
Apr 04, 2019 |
| Last update date |
Jan 01, 2021 |
| Contact name |
Hong Zheng |
| E-mail(s) |
[email protected]
|
| Organization name |
Army Medical University (Third Military Medical University)
|
| Street address |
30 Gaotanyan Street
|
| City |
Chongqing |
| ZIP/Postal code |
400037 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE129323 |
Transcriptome Analysis of Plasmodium ΔCSP stable expressing or control HepG2 cells |
|
| Relations |
| BioSample |
SAMN11340106 |
| SRA |
SRX5635818 |
