DNA Microarrays for Gene Expression Analysis in Brain Tissue and Cell Lines

2011 ◽  
pp. 1-20
Author(s):  
Gustavo A. Barisone ◽  
Elva Díaz
Keyword(s):  
Gene Expression ◽  
Brain Tissue ◽  
Cell Lines ◽  
Expression Analysis ◽  
Dna Microarrays ◽  
Gene Expression Analysis

The application of DNA microarrays in gene expression analysis

2000 ◽  
Vol 78 (3) ◽  
pp. 271-280 ◽  
Author(s):  
Nicole L.W van Hal ◽  
Oscar Vorst ◽  
Adèle M.M.L van Houwelingen ◽  
Esther J Kok ◽  
Ad Peijnenburg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Dna Microarrays ◽  
Gene Expression Analysis

Comprehensive gene expression analysis after ERH gene knockdown in human bladder cancer T24 cell lines

Gene ◽  
2020 ◽  
Vol 738 ◽  
pp. 144475
Author(s):  
Kun Pang ◽  
Lin Hao ◽  
Zhenduo Shi ◽  
Bo Chen ◽  
Huiqing Pang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bladder Cancer ◽  
Cell Lines ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Gene Knockdown ◽  
Human Bladder Cancer ◽  
Human Bladder

Bortezomib Is Effective for Down Regulation of Gene Transcriptions Specifically Expressed in Clonogenic Myeloma Side Population Cells

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 3939-3939
Author(s):  
Miho Nara ◽  
Hiroyuki Tagawa ◽  
Kazuaki Teshima ◽  
Atsushi Watanabe ◽  
Mitsugu Ito ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Cell Lines ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Kinase Inhibitor ◽  
Side Population ◽  
Aurora Kinase ◽  
Aurora Kinase B ◽  
Transporter Family

Abstract Abstract 3939 Background: Multiple myeloma (MM) is characterized by the accumulation of a population of malignant plasma cells within the bone marrow. Cytotoxic chemotherapy-based treatment is not curative, and the disease eventually recurs. Although currently available anti-MM strategies are effective at targeting the bulk of tumor cells, it is not clear that these agents are targeting the tumor-initiating subpopulation, or cancer stem cells. Side Population (SP) cells are an enriched source of cancer-initiating cells with stem cell properties, which have been identified in solid tumors, as well as in hematopoietic malignancies. SP cells express high levels of various members of the ABC transporter family, which are responsible for their drug resistance. A recent our work demonstrated that SP cells in MM have shown to exhibit stem cell like characteristics as well as high tumorigenicity. Therefore, it is worthy to identify gene/proteins specifically expressed in MM SP cells, which could be essential therapeutic targets. Purpose: The aim of this study was to identify genes and transcripts that could serve as molecular markers for targeting the MM SP cells, and to identify candidate agents for the MM SP cells. Experimental design: We used Hoechst 33342 dye to detect the MM SP in five MM cell lines (RPMI 8226, AMO1, KMS-12BM, KMS-11 and JJN3) and eight primary samples. We then tested whether the MM SP cells have stem-like characteristics and performed gene expression analysis to detect genes specifically expressed in the MM SP. On that basis, we tested candidate agents such as an aurora kinase inhibitor (VX-680), a histone methyltransferase inhibitor (DZNep), lenalidomide, thalidomide and a proteasome inhibitor (bortezomib) for their ability to target MM SP cells. Results: We found that clonogenic MM SP cells exhibit “stem cell-like” properties, including self renewal, differentiation and repopulation. Gene expression analysis of MM cell lines and primary samples revealed that, in SP cells, expression of genes related to G2/M phase (e.g. CDC2, CCNB1)-, microtubule attachment (e.g. BIRC5, CENPE, SKA1)-, mitosis or centrosomes (e.g. AURKB, KIF2C, KIF11, KIF15)-, proliferation (e.g. TOP2A, ASPM)-, polycomb (e.g. EZH2, EPC1)- and proteasomes(e.g. UBE2D3, UBE3C, PSMA5)- was significantly stronger in SP than non-SP cells. On that basis, we used VX-680, DZNep, lenalidomide, thalidomide and bortezomib against MM cells. Of these, bortezomib reduced the SP fraction most effectively due to its ability to reduce levels of target gene transcripts including phospho-histone H3, aurora kinase B and EZH2. Finally we tried to examine effects of those candidate agents to “clonogenic ability of SP”, and found that bortezomib possessed the most powerful effects for reduction of SP colonies. These results suggest that bortezomib has a broader range of targets than other agents and could include cell cycle, centrosome, polycomb and proteasome genes/proteins. Conclusion: Our findings are i) the first to identify genes specifically expressed in the MM SP, ii) the first to provide a rationale for treating MM using agents against genes and encoded proteins that are specifically expressed in MM SP cells. Disclosures: Iida: Janssen Pharmaceutical K.K.: Honoraria.

scholarly journals Biological effect of ketamine in urothelial cell lines and global gene expression analysis in the bladders of ketamine-injected mice

2014 ◽  
Vol 11 (2) ◽  
pp. 887-895 ◽  
Author(s):  
CHENG-HUANG SHEN ◽  
SHOU-TSUNG WANG ◽  
YING-RAY LEE ◽  
SHIAU-YUAN LIU ◽  
YI-ZHEN LI ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Expression Analysis ◽  
Biological Effect ◽  
Gene Expression Analysis ◽  
Global Gene Expression ◽  
Urothelial Cell ◽  
Global Gene Expression Analysis

Gene expression analysis of toxicological pathways in TM3 leydig cell lines treated with Ethane dimethanesulfonate

2012 ◽  
Vol 26 (6) ◽  
pp. 213-223 ◽  
Author(s):  
Eun-Hee Lee ◽  
Jung-Hwa Oh ◽  
Young-Sook Lee ◽  
Han-Jin Park ◽  
Mi-Sun Choi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Expression Analysis ◽  
Leydig Cell ◽  
Gene Expression Analysis

scholarly journals Genome Based Search for Reference Genes for Gene Expression Analysis in Oral Cancer: a Data Science Driven Approach

2019 ◽  
Author(s):  
Nehanjali Dwivedi ◽  
Sujan K Dhar ◽  
G Charitha ◽  
Moni Abraham Kuriakose ◽  
Amritha Suresh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Expression Analysis ◽  
Reference Genes ◽  
Data Science ◽  
Gene Expression Analysis ◽  
The Cancer Genome Atlas ◽  
Experimental Conditions ◽  
Statistical Measures ◽  
Different Types

Abstract Background Quantitative real time PCR (qPCR) remains by far the most cost-effective, fast yet sensitive technique to check the gene expression levels in various systems. The traditionally used reference genes over the years were found to be regulated heavily based on sample sources and/or experimental conditions. This paper therefore presents a data science driven -omic approach for selection of reference genes from ~60,000 candidates from The Cancer Genome Atlas (TCGA) and Broad Institute Cancer Cell Line Encyclopaedia (CCLE) for gene expression studies in head and neck squamous cell carcinoma (HNSCC). mRNA-sequencing data of 500 patient samples and 33 cell lines from publicly available databases were analysed to assess stability of genes in terms of multiple statistical measures. A final set of 12 candidate genes were studied in the Indian set of data in Gene Expression Omnibus (GEO) and validated experimentally using qPCR in 35 different types of samples from platforms like drug sensitive and resistant cell lines, normal and tumor samples, fibroblast and epithelial primary culture derived from HNSCC patients from India. Result The study lead to the choice of five most stable reference genes –TYW5, RIC8B, PLEKHA3, CEP57L1 and GPR89B across three experimental platforms. Conclusion In addition to providing a set of five most stable reference genes for future gene expression analysis experiments across different types of samples in HNSCC, the study also presents an objective framework for assessing reference genes for other disease areas as well.

Identification of regulatory pathways across different cell lines (NHBE and PBMC) in COVID-19 patients using transcriptome analysis v1

2021 ◽  
Author(s):  
Lavanya not provided C ◽  
Vidya Niranjan ◽  
Aajnaa not provided Upadhyaya ◽  
Arpita not provided Guha Neogi
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Cell Lines ◽  
Expression Analysis ◽  
Pathway Analysis ◽  
Gene Expression Analysis ◽  
Reference Genome ◽  
Host Cells ◽  
Human Reference Genome ◽  
Regulatory Pathways

The Sars-CoV-2 virus is a previously uncharacterized coronavirus and causative agent of the COVID-19 pandemic. Gene expression analysis followed by pathway analysis helps researchers to find possible key targets present in biological pathways of host cells that are targeted by the SARS-CoV-2 virus. This review considers the peripheral blood mononuclear cell line (PBMC) and the normal human bronchial epithelial (NHBE) cell line, both of which support SARS-CoV-2 viral replication. Pathway analysis between the healthy and patient samples of the respective cell lines shall provide useful insights on the COVID-19 disease. Initially, the datasets from the respective cell lines were collected from the NCBI databank. These datasets underwent further analysis and were mapped and aligned to the human reference genome. This outputs the file in the BAM format. The BAM files along with the human reference genome in the GFF format were uploaded to an open-source software called OmicsBox 2.0 for differential gene expression analysis. This resulted in the generation of a table containing the differentially expressed genes which were upregulated and downregulated. These gene lists were uploaded to various pathway analyzers that map the significant genes to the most significant pathways. In this project, KOBAS 3.0 and Enrichr were used for pathway analysis. The pathways obtained from the above-mentioned pathway analyzers were further narrowed down by manual comparison. It was observed that many pathways were similar between the NHBE and PBMC cell lines. However, they were also different in terms of their overall nature. In this project, many patterns were seen through the pathways obtained, however, further optimization and functionality studies must be performed in order to establish conclusive results on the scope of the COVID-19 disease. Expanding research on the scope of the disease by going back to the basics will generate new and valuable information about the virus. This knowledge will help us combat the disease in a better and appropriate manner.

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