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Series GSE50760 Query DataSets for GSE50760
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
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.
 
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).
 
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
Submission date Sep 11, 2013
Last update date Jun 05, 2024
Contact name Seon-Kyu Kim
E-mail(s) seonkyu@kribb.re.kr
Phone +82-42-879-8107
Organization name Korea Research Institutue of Bioscience & Biotechnology
Department Personalized Genomic Medicine Research Center
Street address 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
City Daejeon
ZIP/Postal code 305-806
Country South Korea
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (54)
GSM1228184 primary colorectal cancer AMC_2-1
GSM1228185 primary colorectal cancer AMC_3-1
GSM1228186 primary colorectal cancer AMC_5-1
Relations
BioProject PRJNA218851
SRA SRP029880

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE50760_RAW.tar 7.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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