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Next Generation Sequencing Facilitates Quantitative Analysis of LAP2α deficient cells and control cells

ABSTRACT: Purpose: The goals of this study are to compare the mRNA profiles of LAP2α deficient human adipose-derived stem cells (hASCs) with that of control hASCs by NGS-derived RNA-seq to screen differentially expressed genes and possible involved pathways. Methods: Total RNA was isolated from hASCs transfected with shLAP2α and shNC. RNA sequencing of control and LAP2α deficient cells (each with 2 biological replicates) was performed using BGISEQ-500 sequencing system. Differentially expressed genes (DEGs) between control and LAP2α deficient cells were screened using NOISeq method. KEGG pathway enrichment analysis and Gene Ontology analysis of DEGs were subsequently conducted. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the cell genome. The scatterplot showed that depletion of LAP2α resulted in the upregulation of 106 genes and downregulation of 91 genes. KEGG pathway analysis suggested that LAP2α knockdown led to the change of several important pathways, including cell cycle, MAPK, and NF-κB signaling pathways that are critically related to cell growth and differentiation. Conclusions: Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue.

ORGANISM(S): Homo sapiens

PROVIDER: GSE138512 | GEO | 2020/07/07

REPOSITORIES: GEO

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Project description:Background: Tomato (Solanum lycopersicum) self-compatibility (SC) is defined as self-pollen tubes that can penetrate their own stigma, elongate in the style and fertilize their own ovules. Self-incompatibility (SI) is defined as self-pollen tubes that are prevented from developing in the style. To determine the influence of gene expression on style self-pollination, a transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles was performed using RNA-sequencing (RNA-seq) data. Results: Transcriptome profiles of 24-h unpollination (UP) and self-pollination (P) styles from SC and SI tomato species were generated using high-throughput next generation sequencing. From the comparison of SC self-pollinated and unpollinated styles, 1341 differentially expressed genes (DEGs) were identified, of which 753 were downregulated and 588 were upregulated. From the comparison of SI self-pollinated and unpollinated styles, 804 DEGs were identified, of which 215 were downregulated and 589 were upregulated. Nine gene ontology (GO) terms were enriched significantly in SC and 78 GO terms were enriched significantly in SI. A total of 105 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified in SC and 80 enriched KEGG pathways were identified in SI, among which “Cysteine and methionine metabolism pathway” and “Plant hormone signal transduction pathway” were significantly enriched in SI. Conclusions: This study is the first global transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles. Advanced bioinformatic analysis of DEGs uncovered the pathways of “Cysteine and methionine metabolism” and “Plant hormone signal transduction”, which are likely to play important roles in the control of pollen tubes growth in SI species. 24-h unpollination (UP) and self-pollination (P) styles mRNA profiles from SC and SI tomato species were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 platform.

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Next Generation Sequencing Facilitates Quantitative Analysis of LAP2α deficient cells and control cells

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