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E-MTAB-4729

ABSTRACT: RNA-seq analysis of 2 cell line models of lung disease (A549 and BEAS-2B) and primary bronchial epithelial cells in Project 3 of Open Targets 020 - Epigenomes of Cell Lines

PROVIDER: E-MTAB-4729 | ExpressionAtlas | 2025-01-23

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-4729-analysis-methods.tsv	Tabular
	E-MTAB-4729-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-4729-coexpressions.tsv.gz	Tabular
	E-MTAB-4729-configuration.xml	Xml
	E-MTAB-4729-factors.xml	Xml

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RNA-seq analysis of 2 cell line models of lung disease (A549 and BEAS-2B) and primary bronchial epithelial cells in Project 3 of Open Targets 020 - Epigenomes of Cell Lines

Project description:This experiment captures the baseline expression of two cell lines (A549, BEAS-2B) selected for Project 3, Open Targets 020 (http://opentargets.org). These cell lines are both possible models for lung disease. In addition, the baseline expression of bronchial epithelial primary cells (NHBE cells) from 3 donors has also been measured. <br> This RNA-seq experiment is being carried out as part of the Open Targets project to identify a gene expression signature of common immortalized cell lines/models. This signature will be used in combination with data from ChIP-seq experiments from the same cell lines against primary cells and tissues. The overall aim of the Open Targets Cell Line Epigenome project is to establish a systematic approach for the determination of human biological and disease relevance through the generation of transcriptomic and epigenomic data in cell lines of interest. Comparison of cell line mRNA expression and epigenome data with existing and newly generated reference data from human tissue and cell types will identify assay systems that will provide greater confidence in translating target biology and compound pharmacology to patients.

2017-07-04 | E-MTAB-4729 | biostudies-arrayexpress

E-MTAB-4101

Project description:RNA-seq analysis of six cell line models for haematopoiesis: Project 1 of Open Targets - Epigenomes of Cell Lines

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MicroRNA levels in non-transformed and transformed lung cells

2014-03-11 | GSE55748 | GEO

E-MTAB-6870

Project description:RNA-seq analysis of several in vitro models of hepatocyte function: Project 4 of Open Targets - Epigenomes of Cell Lines

2025-01-23 | E-MTAB-6870 | ExpressionAtlas

MicroRNA levels in non-transformed and transformed lung cells

Project description:MicroRNA levels in non-transformed BEAS-2B bronchial epithelial cells, two lines of mycoplasma transformed BEAS-2B cells, and A549 lung adenocarcinoma cells were measured. Microarray analyses of 1145 microRNAs in A549 lung adenocarcinoma cells and two other transformed lung cell types relative to BEAS-2B bronchial epithelial cells were performed. 106 miRNAs were down-regulated and 69 miRNAs were up-regulated in all three transformed lines The control cells were the human non-transformed BEAS-2B cells (Lechner JF, LaVeck MA. A serum-free method for culturing normal human bronchial epithelial cells at clonal density. J. Tissue Culture Methods 9: 43-48, 1985). The BEAStra1 and BEAStra2 cells were replicate populations of BEAS-2B cells that were transformed following infection with mycoplasma (Jiang, S., Zhang, S., Langenfeld, J., Lo, S.C., and Rogers, M.B., Mycoplasma infection transforms normal lung cells and induces bone morphogenetic protein 2 expression by post-transcriptional mechanisms. J Cell Biochem. 104(2): 580-594, 2007). A459 lung adenocarcinoma cells were derived from a human lung tumor (Giard DJ, et al. In vitro cultivation of human tumors: establishment of cell lines derived from a series of solid tumors. J. Natl. Cancer Inst. 51: 1417-1423, 1973. PubMed: 4357758).

2014-03-11 | E-GEOD-55748 | biostudies-arrayexpress

E-GEOD-52143

Project description:Changes in global gene expression in lung cancer cell lines A549 (A) and HTB56 (H) [Affymetrix microarrays]

2025-01-24 | E-GEOD-52143 | ExpressionAtlas

E-MTAB-6867

Project description:RNA-seq analysis of several immortalized B cell lines (Namalwa, Daudi, Ramos, Raji, Toledo, ARH-77): Project 6 of Open Targets - Epigenomes of Cell Lines

2025-01-23 | E-MTAB-6867 | ExpressionAtlas

E-GEOD-50627

Project description:transcription profiling by array of stem cells isolated from non-small cell lung cancer cell lines (NCI-H2170 and A549) and normal lung epithelial cell line (PHBEC)

2025-01-24 | E-GEOD-50627 | ExpressionAtlas

Identification of novel metastases-suppressor genes involved in lung cancer brain metastases formation.

Project description:Initial screening for potential metastases suppressors down regulated by methylation was performed using lung cancer cell line models specific for site-specific metastasation. Gene expression profiling and qRT-PCR validations were conducted on tumor tissues from primary lung cancer (LC) and brain metastasis. HERC5 was further characterized for the methylation pattern. Three human lung cancer cell lines H1993, H1395 and were compared to the (SV40)-transformed human bronchial epithelial cell line BEAS-2B in order to find genes, which might be specifically involved in brain metastasis formation. The cell lines were treated with 5-Aza-2'-deoxycytidine in order to find genes potentially down regulated by methylation. The non-tumorigenic cell line BEAS-2B was used to control for stress response after the treatment with 5-Aza-2'-deoxycytidine.

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Uncovering the divergent epigenetic background of KRAS-mutant NSCLC in mouse and human cell lines

Project description:Illumina miRNA-seq method to uncover the expression profile of NSCLC in-vitro experimental models consisting of cell lines A549, H460 compared to healthy BEAS-2B cell line, and lung tissue (NSCLC and paired normal) from urethane treated 6-week-old FVB/NJ mice. We aimed to uncover the divergent epigenetic background of KRAS-mutant NSCLC in mouse and human cell lines, extensively used as biological models in relevant research. To that end, we have comprehensively mapped the functional miRNA and lncRNA landscape of human (A549 and H460) and mouse (experimentally developed LUAD) NSCLC models and correlated current results with LRF/ZBTB7A expression

2023-12-25 | GSE251697 | GEO

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