Project description:To investigate the global genes regulated by lncRNA-SLCC1(RP11-400N13.2), high-throughput mRNA sequencing (RNA-Seq) was performed to compare the expression profile between DLD-1 cells transfected with control siRNA or lncSLCC1 siRNA.
Project description:Knockdown of Sox2 in SW620 colorectal cancer cells decrease their growth rates in vitro and in vivo in xenograft models. We used microarrays to detail the global programme of gene expression in Sox2 Knockdown sw620 cells compared with mock knockdown sw620 cells Sox2 knockdown sw620 cells and and mock knockdown sw620 cells were cultured in RPMI 1640 cell culture media for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the genes regulated by Sox2 in colorectal cell lines and end (T4) of gastrulation.
Project description:Downregulations of TCAM1P-004 and RP11-598D14.1 were frequently observed in HCC tumors as compared to adjacent non-tumor tissues. To further study the molecular functions of TCAM1P-004 and RP11-598D14.1, we attempted to identify the gene targets regulated by either lncRNAs. Knockdown of TCAM1P-004 or RP11-598D14.1 were achieved by transduction of lentivirus carrying respective shRNAs in non-tumor hepatocyte MIHA cells. Diffferentially expressed genes after knockdown of the lncRNAs were compared to cells tranduced with lentivirus carrying scramble shRNAs.
Project description: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.
Project description:The study identifies a set of genes through functional selection in an orthotopic colorectal cancer mouse model that play an important role in mediating colorectal cancer liver metastasis. We look at the gene profiling of metastatic colorectal cancer cells (L1 and L2) and non-mestastatic colorectal cancer cells (sw620 and sw480) using Affymetrix U133A oligonucleotide arrays. 4 samples (each with triplicates) were analyzed. Genes with a fold-change ≥2 (P<0.05) were selected.