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| Status |
Public on Aug 11, 2023 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of CreAlbMYC and CreAlbScarb2F/FMYC mice liver tissue Transcriptomes |
| Organism |
Mus musculus |
| 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 liver tissue of CreAlbMYC and CreAlbScarb2F/FMYC mice by using RNA-seq.
Methods: CreAlbMYC and CreAlbScarb2F/FMYC liver tissue mRNA profiles were generated by deep sequencing, using Illumina Novaseq 6000. 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, DEGseq was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG .
Conclusions:Our study represents the first detailed analysis of CreAlbMYC and CreAlbScarb2F/FMYC liver tissue 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 |
CreAlbMYC and CreAlbScarb2F/FMYC liver tissue mRNA profiles were generated by deep sequencing using Illumina Novaseq 6000..
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| Contributor(s) |
Li K, Jiang J, Wang F, Gao Y, Xue S |
| Citation(s) |
37739936 |
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| Submission date |
Oct 13, 2021 |
| Last update date |
Oct 03, 2023 |
| Contact name |
Yang Gao |
| E-mail(s) |
yxgyang@126.com
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| 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
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| City |
Beijing |
| ZIP/Postal code |
100050 |
| Country |
China |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (2) |
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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. |
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| Relations |
| BioProject |
PRJNA770989 |
| SRA |
SRP341216 |
