 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 14, 2018 |
| Title |
RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Long non-coding RNA (lncRNA) have been implicated in human pathology, however, their roles in colorectal carcinogenesis has not been fully elucidated. In the current study, whole-transcriptome was analyzed in 3 pairs of colorectal cancer (CRC) and matched normal mucosa (NM) by RNA sequencing (RNA-seq). Followed by confirmation using the Cancer Genome Atlas (TCGA) dataset, we identified 27 up-regulated and 22 down-regulated lncRNAs in CRC. Up-regulation of four lncRNAs, hereby named colorectal cancer associated lncRNA (CRCAL)-1 [AC021218.2], CRCAL-2 [LINC00858], CRCAL-3 [RP11-138J23.1] and CRCAL-4 [RP11-435O5.2], was further validated by real-time RT-PCR in 139 colorectal neoplasms and matched NM tissues. Knockdown of CRCAL-3 and CRCAL-4 in colon cancer cells reduced cell viability and colony formation ability, and induced cell cycle arrest. TCGA dataset supported the associations of CRCAL-3 and CRCAL-4 with cell cycle and revealed a co-expression network comprising dysregulated lncRNAs associated with protein-coding genes. In conclusion, RNA-seq identified numbers of novel lncRNAs dysregulated in CRC. In vitro experiments and GO term enrichment analysis indicated the functional relevance of CRCAL-3 and CRCAL-4 in association with cell cycle. Our data highlight the capability of RNA-seq to discover novel lncRNAs involved in human carcinogenesis, which may serve as alternative biomarkers and/or molecular treatment targets.
|
| |
|
| Overall design |
6 total samples consisting of 3 matched pairs of colorectal cancer (CRC) and matched normal mucosa (NM)
|
| |
|
| Contributor(s) |
Yamada A, Yu P, Lin W, Okugawa Y, Boland CR, Goel A |
| Citation(s) |
29330370 |
| |
| Submission date |
Sep 25, 2017 |
| Last update date |
Mar 16, 2023 |
| Contact name |
Nicole Baldwin |
| E-mail(s) |
[email protected]
|
| Organization name |
Baylor Research Institute
|
| Street address |
3434 Live Oak St
|
| City |
Dallas |
| ZIP/Postal code |
75204 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (6)
|
|
| Relations |
| BioProject |
PRJNA411984 |
| SRA |
SRP118775 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE104178_Differentially_expressed_lncRNAs_Wei_s_analysis_11052014.csv.gz |
1.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...