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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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3D Laparoscopy Versus 2D Laparoscopy

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3D vs . 2D culture of HUASMC

Project description:3D vs . 2D culture of HUASMC

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Project description:In these microarray experiments, we characterize the gene expression of mammary epithelial cells (MCF10A cells) grown in either a traditional monolayer cell culture setting (2D) or on Matrigel, which induces single MCF10A cells to form organized acinar structures (3D). Morphogenesis of mammary epithelial cells into organized acinar structures in vitro is accompanied by widespread changes in gene expression patterns, including a substantial decrease in expression of Myc. The purpose of this study was to analyze the impact of morphogenesis and organization on gene expression with respect to changes in overall gene expression and Myc target gene expression. MCF10A cells were cultured in 2D for either 2 or 5 days (3 biological replicates each) or in 3D for 8 or 16 days (3 or 5 biological replicates, respectively)

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Expression data of two human cancer cell lines cultivated in 2-dimensional (2D) vs. 3-dimensional (3D) cell culture

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Project description:We examined whether SATB1 functions as a global gene regulator in order to maintain the aggressive phenotype of the MDA-MB-231 cell line. We compared the gene expression profiles between control_shRNA-MDA-MB-231 cells, which express SATB1 at high levels, and SATB1_shRNA1-MDA-MB-231 in which the level of SATB1 was greatly downregulated by RNAi technology. This comparative studies were performed using two different platforms (Codelink and Affymetrix genechip) with two culture conditions either on plastic dish (2D) or on matrigel (3D) which allows cells to form a breast-like morphology only for non-aggressive cells. Keywords: Comparative studies on Control_shRNA and SATB1_shRNA1 expressing MDA-MB-231 from 2D or 3D culture. We examined control_shRNA-MDA-MB-231 cells and SATB1_shRNA1-MDA-MB-231 cells under two culture condition;on plastic dish(2D culture) and on Matrigel coated dish(3D culture). When SATB1 was depleted by RNAi technology, these normally aggressive cells exhibited normal breast like morphology on 3D. We used two different microarray platforms (Codelink and Affymetrix) to make expression data. Initial analysis of data and cross-platform comparison were performed using Codelink expression analysis and GeneSpring software. We provide ratio for control_shRNA/SATB1_shRNA1-MDA-MB-231 cells for 2D and 3D on this series.

2010-05-26 | E-GEOD-5417 | biostudies-arrayexpress

2D and 3D Madin-Darby Canine Kidney Cell Type II cell line response to hepatocyte growth factor

Project description:Analysis of 2D (transwell) and 3D (collagen type I) cultured MDCK cells and HGF (a MAPK activator). Traditional 2D cultures are fast and inexpensive but do no mimic natural niche/cell environment as well as the more laborious and costly 3D-cultures. 3D cultures, arguably, are better models for the study of developmental processes, such as tubulogenesis. Epithelial organs (such as kidney) develop via tubulogenesis, a process, at least in part, regulated by MAPK signaling. Therefore, 2D and 3D cells also treated with HGF plus MAPK inhibitors. Results provide insights into differential response to HGF-induced tubulogenesis depending on cell culture conditions (2D vs. 3D). 29 samples total: 2D and 3D control (untreated) in quadruplicate, respectively; 2D and 3D + HGF in quadruplicate, respectively; 2D + HGF + PD-98059 in quadruplicate; 3D + HGF + PD-98059 in triplicate; 2D + HGF + U0126 in triplicate; and 3D + HGF + U0126 in triplicate.

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