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Status |
Public on Aug 31, 2014 |
Title |
Gene expression profiling study by RNA-seq in colorectal cancer |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
The objective of this study is to identify a prognostic signature in colorectal cancer (CRC) patients with diverse progression and heterogeneity of CRCs. We generated RNA-seq data of 54 samples (normal colon, primary CRC, and liver metastasis) from 18 CRC patients and, from the RNA-seq data, identified significant genes associated with aggressiveness of CRC. Through diverse statistical methods including generalized linear model likelihood ratio test, two significantly activated regulators were identified. In the validation cohorts, two activated regulators were independent risk factors and potential chemotherapy-sensitive agenets in colorectal cancers.
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Overall design |
RNA-seq data of 54 samples (normal colon, primary CRC, and liver metastasis) were generated from 18 CRC patients. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x100 bp) using Hiseq-2000 (Illumina).
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Contributor(s) |
Kim J, Kim S, Kim S, Kim J |
Citation(s) |
- Kim SK, Kim SY, Kim JH, Roh SA et al. A nineteen gene-based risk score classifier predicts prognosis of colorectal cancer patients. Mol Oncol 2014 Dec;8(8):1653-66. PMID: 25049118
- Kim JC, Ha YJ, Tak KH, Roh SA et al. Complex Behavior of ALDH1A1 and IGFBP1 in Liver Metastasis from a Colorectal Cancer. PLoS One 2016;11(5):e0155160. PMID: 27152521
- Kim SK, Kim SY, Kim CW, Roh SA et al. A prognostic index based on an eleven gene signature to predict systemic recurrences in colorectal cancer. Exp Mol Med 2019 Oct 2;51(10):1-12. PMID: 31578316
- Ha YJ, Park SH, Tak KH, Lee JL et al. CILP2 is a potential biomarker for the prediction and therapeutic target of peritoneal metastases in colorectal cancer. Sci Rep 2024 May 31;14(1):12487. PMID: 38816545
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Submission date |
Sep 11, 2013 |
Last update date |
Jun 05, 2024 |
Contact name |
Seon-Kyu Kim |
E-mail(s) |
seonkyu@kribb.re.kr
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Phone |
+82-42-879-8107
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Organization name |
Korea Research Institutue of Bioscience & Biotechnology
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Department |
Personalized Genomic Medicine Research Center
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Street address |
125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
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City |
Daejeon |
ZIP/Postal code |
305-806 |
Country |
South Korea |
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Platforms (1) |
GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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Samples (54)
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Relations |
BioProject |
PRJNA218851 |
SRA |
SRP029880 |
Supplementary file |
Size |
Download |
File type/resource |
GSE50760_RAW.tar |
7.4 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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