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| Status |
Public on Dec 31, 2020 |
| Title |
Transcriptome Analysis of Plasmodium ΔCSP stable expressing or control HepG2 cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose:To understand the change in transcriptome for the overxepression of ΔCSP in HepG2 cells.
Methods:Total RNAs of ΔCSP stable expressing or control HepG2 cells were extracted using TRIzol (Invitrogen), following the manufacturer's instructions. RNA-seq and bioinformatic data analysis were performed by Shanghai Sangon Bio Ltd. Briefly, sequencing libraries were generated using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Vazyme Biotech, Nanjing, China) following manufacturer's recommendations and were sequenced on HiSeq XTen sequencers (Illumina, San Diego, CA). Raw reads in FASTQ format were subjected to quality control using FastQC. RNA-seq reads were aligned to the reference genome using Bowtie. Uniquely mapped reads were used for further analysis. Gene expression levels are expressed as TPM (Transcripts per million reads) and differences in gene expression were calculated with rSeq.
Results:There were 492 genes differentially expressed in ΔCSP-overexpressing HepG2 cells compare to the control group respectively (fold change >2 or < 0.5).
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| Overall design |
mRNA profiles of ΔCSP stable expressing or control HepG2 cells were generated by deep sequencing in triplicate, using illumina HiSeq XTen platform.
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| Contributor(s) |
Zheng H, Lu X, Li K, Zhu F, Zhao C, Liu T, Ding Y, Fu Y, Dai J, Wu Y, Xu W |
| Citation(s) |
35222391 |
| Submission date |
Apr 04, 2019 |
| Last update date |
Mar 04, 2022 |
| Contact name |
Hong Zheng |
| E-mail(s) |
ziecoe@tmmu.edu.cn
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| Organization name |
Army Medical University (Third Military Medical University)
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| Street address |
30 Gaotanyan Street
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| City |
Chongqing |
| ZIP/Postal code |
400037 |
| Country |
China |
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| Platforms (1) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA530961 |
| SRA |
SRP190844 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE129323_RAW.tar |
1.6 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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