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Next Generation Sequencing Facilitates Quantitative Analysis of the transcriptomes of RAW264.7 cell in 3D and 2D culture

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of the transcriptomes of RAW264.7 cell in 3D and 2D culture

PROVIDER: PRJNA776275 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16636534_1.fastq.gz	Fastqsanger.gz
	SRR16636534_2.fastq.gz	Fastqsanger.gz
	SRR16636535_1.fastq.gz	Fastqsanger.gz
	SRR16636535_2.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of the transcriptomes of RAW264.7 cell in 3D and 2D culture

Project description:Purpose: the goal of this study is to detect and compare the transcriptome expression of mouse macrophages cultured in 3D and 2D environments, and find the effect of 3D culture on macrophages compared with traditional 2D culture. Methods: Total RNA was extracted from purified and untreated RAW264.7 cells from 3D and 2D culture systems using TRIzol. The RNA samples were analyzed using Whole Genome Oligo Microarrays. After RNA had been hybridized to the microarray, it was washed and scanned, and data were extracted using Agilent Feature Extraction Software. Gene expression data were generated using Affymetrix GeneChip Human Genome U133 Plus 2.0 on an Affymetrix 3000 instrument running Gene‑Chip operating software. Result: RNA-sequencing (RNA-seq) revealed that after 24 h of culture under the same conditions, 3D-cultured macrophages showed significant differences in gene expression. RNA-seq detected 18580 genes in the 2D group and 15777 genes in the 3D group, among which 6762 were differentially expressed (|log2(fold change)| >= 1, padj < 0.05) in both 3D and 2D groups. A total of 5949 genes were downregulated and 813 were upregulated. Conclusion: Our study represents the first detailed analysis of the effect of 3D culture on mouse macrophages, and the results showed that compared with traditional 2D culture, the gene expression of macrophages under 3D culture was significantly changed.These findings are therefore worthy of further investigation and verification, and provide novel avenues for future research in cytology and macrophages.

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