Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA388012 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene expression data were collected by RNA-seq from HCT-116 cells in the presence or absence of siRNA targeting APC and 1,376 transcripts changed in expression following APC silencing were identified relative to scrambled siRNA-transfected and untreated controls.
2018-05-24 | GSE99263 | GEO
Project description:Anti-APC ChIP-seq data were collected from HCT-116 cells and 44,771 genomic sequences were found to be enriched.
2017-12-13 | GSE103894 | GEO
Project description:Anti-APC ChIP-seq data were collected from HCT-116 cells and 3,985 genomic sequences were found to be enriched in both independent biological replicates.
2018-05-24 | GSE99262 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived HCT-116 cell transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: HCT-116 cell mRNA profiles of HCT-116-GOLPH3-Vector and HCT-116-GOLPH3-Overepression were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: RNA sequencing (RNA-seq) was used to investigate gene expression in HCT-116-PMSCV-Vector and HCT-116-PMSCV GOLPH3 cells, while Gene Ontology (GO) was used to annotate the various functional genes. By comparing the differentially expressed genes, we noticed that GOLPH3 was associated with EMT. Gene set enrichment analysis (GSEA) analysis of the RNA-seq results based on the GSE77953 dataset was performed to investigate the biological functions of HCT-116-PMSCV-Vector and HCT-116-PMSCV-GOLPH3 cells. The findings suggested that GOLPH3 expression was positively associated with colon cancer cell autophagy. Signal pathway enrichment was next analyzed based on the differential expression of genes between HCT-116-PMSCV-Vector and HCT-116-PMSCV-GOLPH3 cells, as examined by RNA-seq. Notably, GOLPH3 has correlated with the PI3K/Akt signaling pathway. Conclusions: Our study represents the first detailed analysis of HCT-116 cell transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2022-02-23 | GSE196875 | GEO
Project description:UCRs expression signature of HCT-116 cell lines versus HCT-116 cell line treated with DNA methylation inhibitor 5-aza-2'-deoxycytidine
2010-03-09 | E-MTAB-196 | biostudies-arrayexpress
Project description:Efffects of silencing ZBTB4, mSin3a/mSin3b on HCT 116 human colon carcinoma cell lines for 48 hours
2008-03-31 | E-MEXP-1509 | biostudies-arrayexpress
Project description:Purpose: Assess the transcriptional changes induced upon RAB7 knock-down in melanoma (SK-Mel-28 and UACC-62) and in colon cancer (HCT-116) cell lines. Methods: mRNA profiles of tumor cell lines (SK-Mel-28, UACC-62, HCT-116) stably expressing scrambled shRNA or RAB7 shRNA (harvested at day 3 after lentiviral infection) were generated by deep sequencing, using three biological replicates per condition. The sequence reads that passed quality filters were analyzed with TopHat and Cufflinks. Validation of induced / silenced genes was performed by western blot. Results show a differential impact of RAB7 expression in the transcriptomic profile of melanoma vs non-melanoma cell lines, and support a lineage-specific role of this small GTPase in melanoma. Examination of the mRNA profiles RAB7-depleted vs wild type cells, performed in parallel in 3 different tumor cell lines (Melanomas: SK-Mel-28 and UACC-62, Non-melanoma: HCT-116) harvested at day 3 after lentiviral infection.
2014-04-20 | E-GEOD-42735 | biostudies-arrayexpress
Project description:Expression data from colorectal cancer cell line HCT-116
| PRJNA387397 | ENA
Project description:Genome-wide profiling of histone 3 lysine 4 trimethylation is used for identification of microRNA transcriptional start sites. Various cell types allow a broad range detection of putative promoters rather independent of tissue specific expression patterns. These data are used for identification of aberrant epigenetic regulation at the respective regions. 11 samples total: 3 primary B-cell samples (1 chronic lymphocytic leukemia [CLL] and 2 healthy controls), 2 CLL related cell lines -/+ 5-aza-2M-bM-^@M-^Y-deoxycytidine (DAC) treatment (Mec-1, EHEB), T-lymphoid cell line JURKAT, myeloid cell line HL-60, colon cancer cell line HCT-116 wild type and double knock out; H3K4me3 enriched vs. input
2012-05-30 | E-GEOD-33305 | biostudies-arrayexpress