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Series GSE129323 Query DataSets for GSE129323
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
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).
 
Overall design mRNA profiles of ΔCSP stable expressing or control HepG2 cells were generated by deep sequencing in triplicate, using illumina HiSeq XTen platform.
 
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) [email protected]
Organization name Army Medical University (Third Military Medical University)
Street address 30 Gaotanyan Street
City Chongqing
ZIP/Postal code 400037
Country China
 
Platforms (1)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (6)
GSM3705209 Control1
GSM3705210 Control2
GSM3705211 Control3
Relations
BioProject PRJNA530961
SRA SRP190844

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE129323_RAW.tar 1.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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