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| Status |
Public on Aug 11, 2023 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of CON and PMB treatment HepG2 cells Transcriptomes |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in CON and PMB treatment cells by using RNA-seq
Methods: CON and PMB treatment cells mRNA profiles were generated by deep sequencing, using Illumina Novaseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 , IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, EdgeR software was used for differential gene expression analysis and Function Enrichment Analysis including GO enrichment analysis and KEGG .
Conclusions: Our study represents detailed analysis of CON and PMB cells transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
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| Overall design |
CON and PMB cells mRNA profiles were generated by deep sequencing, in triplicate, using Illumina Novaseq 6000.
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| Contributor(s) |
Li K, Jiang J, Wang F, Gao Y, Xue S |
| Citation(s) |
37739936 |
| |
| Submission date |
Oct 13, 2021 |
| Last update date |
Oct 03, 2023 |
| Contact name |
Yang Gao |
| E-mail(s) |
yxgyang@126.com
|
| Phone |
18238837867
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| Organization name |
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College
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| Street address |
Dongcheng District, Tiantan Xili
|
| City |
Beijing |
| ZIP/Postal code |
100050 |
| Country |
China |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE185844 |
Scavenger Receptor SCARB2 Drives Hepatic Carcinoma Initiation by Enhancing MYC Transcriptional Activity and Supporting Cancer Stem Cell Traits. |
|
| Relations |
| BioProject |
PRJNA770983 |
| SRA |
SRP341214 |
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