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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 02, 2019 |
| Title |
Transcriptome Analysis of Huh7 cells Infected with Adenovirus Overexpression GSTZ1 or PCK1 |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose:To understand the change in cellular metabolism and function for the overxepression of GSTZ1 or PCK1 in hepatoma cells. Methods:Total RNAs of AdGFP- , AdGSTZ1-, or AdPCK1-infected Huh7 cells were extracted using TRIzol (Invitrogen), following the manufacturer’s instructions. RNA-seq and bioinformatic data analysis were performed by Shanghai Novel Bio Ltd. Briefly, strand-specific RNA-seq libraries were prepared using the Total RNA-seq (H/M/R) Library Prep Kit (Vazyme Biotech, Nanjing, China) and were sequenced on Ion Torrent Proton sequencing platform. 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 RPKM (reads per kilobase per million reads) and differences in gene expression were calculated with rSeq. Results:There were 498 genes differentially expressed in AdPCK1-infected Huh 7 cells, 513 genes differentially expressed in AdGSTZ1-infected Huh 7 cells compare to the GFP control group respectively (fold change >1.5 or < 0.667; FDR < 0.05).
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| Overall design |
mRNA profiles of AdGFP1, AdGSTZ1- or AdPCK1-infected Huh 7 cells were generated by deep sequencing in triplicate, using Ion Torrent Proton sequencing platform.
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| Contributor(s) |
Tang N, Huang A, Wang K, Tuo L, Xiang J, Yang Y, Yang F, Liang L, Li J |
| Citation(s) |
30717766, 30619751, 31267557, 31782257, 32181286 |
| Submission date |
Jul 27, 2018 |
| Last update date |
Mar 23, 2020 |
| Contact name |
tang ni |
| E-mail(s) |
wangkai.virus@gmail.com
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| Organization name |
Chongqing Medical University
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| Street address |
yixueyuan Road NO.1
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| City |
chongqing |
| ZIP/Postal code |
400016 |
| Country |
China |
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| Platforms (1) |
| GPL17303 |
Ion Torrent Proton (Homo sapiens) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA483237 |
| SRA |
SRP155565 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE117822_All_Counts.txt.gz |
449.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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