Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Effects of hnRNP A1 on gene expression in oral squamous cell carcinoma

ABSTRACT: To find the discover target genes regulated by hnRNP A1 in oral squamous cell carcinoma, NimbleGen 12x135K microarrays were used to find the gene expression changes between hnRNP A1 or non-specific (NS) siRNA treated oral cancer cells. Cal27 cells were treated with hnRNP A1 or non-specific (NS) siRNA twice in a 48-hour interval. After 96 hours, total RNAs were collected for microarray assay. Total RNAs from hnRNP A1 knockdown (3 samples) or NS siRNA treated cells (3 samples) were used for chip experiment (6 chips). Each chip measures the expression levels of human 45,033 genes. NimbleGen One-Color DNA Labeling Kit was used for sample labeling. Hybridization was performed in NimbleGen Hybridization System. After washing, slides were scanned with Axon GenePix 4000B scanner. Data was extracted and normalized using NimbleScan v2.5 Software.

ORGANISM(S): Homo sapiens

SUBMITTER: Rong Jia

PROVIDER: E-GEOD-57819 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Glioblastoma multiforme (GBM) is the most prevalent type of adult brain tumor, and one of the deadliest tumors known to mankind. The genetic understanding of GBM is, however, limited, and the molecular mechanisms which facilitate GBM cell survival and growth within the tumor microenvironment are largely unknown. We applied digital karyotyping and single nucleotide polymorphism (SNP) arrays to screen for copy number changes in GBM samples and found that the most frequently amplified region is at chromosome 7p11.2. The high resolution of digital karyotyping and SNP arrays permits the precise delineation of amplicon boundaries and has enabled identification of the minimal region of amplification at 7p11.2, which contains two genes, EGFR and SEC61?. SEC61? encodes a subunit of a heterotrimeric protein channel located in the endoplasmic reticulum (ER). In addition to its high frequency of gene amplification in GBMs, SEC61? is also remarkably overexpressed in 77% of GBMs, but not in lower-grade gliomas. The siRNA-mediated knockdown of SEC61? expression in tumor cells led to growth suppression and apoptosis. Furthermore, we showed that pharmacological ER stress agents induce SEC61? expression in GBM cells. Together, these results indicate that aberrant expression of SEC61? serves significant roles in GBM cell survival, likely via a mechanism that is involved in the cytoprotective ER stress-adaptive response to the tumor microenvironment. hSETD1A was silenced in HCT116 cells using retrovirus harboring shRNA specifically against the hSETD1A gene. 10?g RNA was reverse transcribed to cDNA using the Applied Biosystems High Capacity cDNA Reverse Transcription kit according to the manufacturer’s instructions (Applied Biosystems). cDNA products were treated with 100ng RNaseA and then purified using the Qiagen PCR purification kit according to the manufacturer’s instructions. NimbleGen Human Gene Expression array was purchased from Roche Applied Sciences. cDNA samples were labeled, Cy3 hybridized, and processed at the FSU NimbleGen Microarray Facility at Florida State University.

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Effects of hnRNP A1 on gene expression in oral squamous cell carcinoma

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