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Expression data of hepatocellular carcinoma and adjacent liver tissues

ABSTRACT: To identify therapeutic targets with high specificity to HCC, we searched for genes significantly up-regulated in HCC over corresponding non-tumor liver using high-density microarrays Keywords: disease state analysis HCC and surrounding non-tumor liver tissue samples were collected from 10 cases who underwent liver resection for HCC at National Cancer Center Hospital (Tokyo, Japan). One µg of total RNA was converted to end-labeled cRNA using the Whole Transcript Sense Target Labeling kit (Affymetrix, Santa Clara, CA). The fluorescent cRNA probes were hybridized to Human Exon 1.0 ST arrays (Affymetrix), as instructed by the supplier.

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PROVIDER: S-DIXA-D-1013 | biostudies-other |

REPOSITORIES: biostudies-other

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Expression data of hepatocellular carcinoma and adjacent liver tissues

2010-06-15 | GSE12941 | GEO

Expression data of hepatocellular carcinoma and adjacent liver tissues

Project description:To identify therapeutic targets with high specificity to HCC, we searched for genes significantly up-regulated in HCC over corresponding non-tumor liver using high-density microarrays Keywords: disease state analysis HCC and surrounding non-tumor liver tissue samples were collected from 10 cases who underwent liver resection for HCC at National Cancer Center Hospital (Tokyo, Japan). One µg of total RNA was converted to end-labeled cRNA using the Whole Transcript Sense Target Labeling kit (Affymetrix, Santa Clara, CA). The fluorescent cRNA probes were hybridized to Human Exon 1.0 ST arrays (Affymetrix), as instructed by the supplier.

2010-06-15 | E-GEOD-12941 | biostudies-arrayexpress

Genome-Wide Extrachromosomal Circular DNA Profiling of Paired Hepatocellular Carcinoma and Adjacent Liver Tissues.

Project description:Hepatocellular carcinoma (HCC) develops through multiple mechanisms. While recent studies have shown the presence of extrachromosomal circular DNA (eccDNA) in most cancer types, the eccDNA expression pattern and its association with HCC remain obscure. We aimed to investigate this problem. The genome-wide eccDNA profiles of eight paired HCC and adjacent non-tumor tissue samples were comprehensively elucidated based on Circle-seq, and they were further cross-analyzed with the RNA sequencing data to determine the association between eccDNA expression and transcriptome dysregulation. A total of 60,423 unique eccDNA types were identified. Most of the detected eccDNAs were smaller than 1 kb, with a length up to 182,363 bp and a mean sizes of 674 bp (non-tumor) and 813 bp (tumor), showing a greater association with gene-rich rather than with gene-poor regions. Although there was no statistical difference in length and chromosome distribution, the eccDNA patterns between HCC and adjacent non-tumor tissues showed significant differences at both the chromosomal and single gene levels. Five of the eight HCC tissues showed significantly higher amounts of chromosome 22-derived eccDNA expression compared to the non-tumor tissue. Furthermore, two genes, SLC16A3 and BAIAP2L2, with a higher transcription level in tumor tissues, were related to eccDNAs exclusively detected in three HCC samples and were negatively associated with survival rates in HCC cohorts from public databases. These results indicate the existence and massive heterogeneity of eccDNAs in HCC and adjacent liver tissues, and suggest their potential association with dysregulated gene expression.

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Expression data from hepatocellular carcinoma and adjacent normal liver tissue

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Expression data from hepatocellular carcinoma and adjacent normal liver tissue

Project description:Assay of gene expression pattern differences between liver cancer tissue and normal liver tissue from the same mouse by microarray in 4 separate mice injected with recombinant adeno-associated viral (AAV) vector 4 Mice (M24, M48, M50, M60) were necropsied at 18 months post-injection of AAV-vector, and livers removed. Tumor tissue and adjacent normal tissue were identified and dissected for RNA extraction.

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RNA-Seq expression profiling of hepatocellular carcinoma and adjacent non-tumor liver tissues

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