RNA-seq of CRC tissues
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE144259 | GEO | 2020/01/27
REPOSITORIES: GEO
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Project description:ArrayStar Human LncRNA/mRNA Expression Microarray Version 3.0 was used to detect lncRNA expression in CRC tissues compared with their matched non-tumoral tissues. Here we report significantly up-regulated as well as down-regulated lncRNAs in CRC tissues compared with their matched non-tumoral tissues.
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Project description:The prognosis of colorectal cancer (CRC) stage II and III patients is still a challenge due to the difficulties of finding robust biomarkers and assays. The majority of published gene signatures of CRC have been generated on frozen colorectal tissues. Because collection of fresh frozen tissues is not routine and the quantity and quality of RNA derived from formalin-fixed paraffin-embedded (FFPE) tissues is vastly inferior to that derived from fresh frozen tissue, a clinical test for improving staging of colon cancer will need to be designed for FFPE tissues in order to be widely applicable. We have designed a custom Nanostring nCounter assay for quantitative assessment of expression of 414 gene elements consisting of multiple published gene signatures for colon cancer prognosis, and systematically compared the gene expression quantification between nCounter data from FFPE and Affymetrix microarray array data from matched frozen tissues using 414 genes. For microarray studies, representative sections of fresh tissue specimens were flash frozen in liquid nitrogen and stored at â80°C until RNA isolation. RNA was purified from tissue sections containing >80% epithelial tumor tissue using RNeasy (QIAGEN, Valencia, CA) according to manufacturerâs instructions. Samples were hybridized to Affymetrix arrays Human Genome U133 Plus 2.0 GeneChip Expression Arrays, Santa Clara, CA). The samples included four healthy control patient tissues, 12 stage I, 17 stage II, 20 stage III and 15 stage IV CRC patient tissues. Please note that only the *matched.csv files containing matched 414 genes' microarray and nanostring data are provided without the nanostring experimental descriptions. The matching samples between GSE62932 and the Nanostring study are indicated in the matching_samples.txt.
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Project description:circRNA expression in CRC and matched non-tumor tissues
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