Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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A Long Noncoding RNA Acts as a Tumor Promoter in Hepatocellular Carcinoma

ABSTRACT: Many long noncoding RNAs are involved in cancer development and progression. Here, we utilized high-throughput microarray to compare the expression difference of transcriptome between the LINC01225 stable knockdown SMCC7721 cells and mock empty plasmid treated SMCC7721 cells; the LINC01225 stable knockdown MHCC97H cells and mock empty plasmid treated MHCC97H cells. These altered genes are involved in tumorigenesis through diverse mechanisms. The present study reveals that LINC01225 functions as a tumor promoter in Hepatocellular Carcinoma. LINC01225 stable knockdown cells were compared to mock empty plasmid treated cells. In addition expression of genes in untreated SMCC7721 cells was detected, we performed a comparison between mock empty plasmid treated SMCC7721 cells and untreated SMCC7721 cells to determine that no confounding factors were brought in. The Agilent human lncRNA+mRNA Array V4.0 were used to perform the analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: Xiaochen Wang

PROVIDER: E-MTAB-3833 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Sorghum (Sorghum bicolor) is one of the world's most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. In this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of S. propinquum with special emphasis on rhizome development. A total of 548 tissue-enriched genes were detected, including 31 and 114 unique genes that were predominantly expressed in the rhizome tips (RT) and internodes (RI), respectively. Further GO analysis indicated that the functions of these tissue-enriched genes corresponded to their characteristic biological processes. A few distinct cis-elements, including ABA-responsive RY repeat CATGCA, sugar-repressive TTATCC, and GA-responsive TAACAA, were found to be prevalent in RT-enriched genes, implying an important role in rhizome growth and development. Comprehensive comparative analysis of these rhizome-enriched genes and rhizome-specific genes previously identified in S. propinquum indicated that phytohormones, including ABA, GA, and SA, are key regulators of gene expression during rhizome development. Co-localization of rhizome-enriched genes with rhizome-related QTLs in rice and sorghum generated functional candidates for future cloning of genes associated with rhizome growth and development. In conclusion, a whole rice genome oligonucleotide microarray was used to profile gene expression across five tissues of the perennial wild sorghum S. propinquum. Expression patterns of the five tissues were consistent with the different functions of each organ, and RT- and RI-enriched genes revealed clues regarding molecular mechanisms of rhizome development. Plant hormones, including ABA, GA, and SA, function as key regulators of rhizome gene expression and development. To shed further light on the identities of rhizome-specific genes, rhizome-enriched candidates were identified using QTL co-localization and comparative analysis. In this study, the specific gene expression patterns across five tissues, including rhizome tip (RT, distal 1 cm of the young rhizome), rhizome internodes (RI), shoot tip (ST, distal 5 mm of the tiller after removing all leaves), shoot internodes (SI) and young leaf (YL) in Sorghum propinquum, especially in the rhizome, were characterized by using a rice genome array. Three independent biological replicates for each tissue from individual plants were performed. The reference was equivalent to a mix of the 5 tissues.

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A Long Noncoding RNA Acts as a Tumor Promoter in Hepatocellular Carcinoma

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