Project description:Transcriptional profiling of HT-29 human colon cancer cells transfected with non-targeting control (NTC) siRNA and two different siRNA sequences against CDK8 (siCDK8-1 and siCDK8-2).
Project description:Gene Expression Profiling of HT-29 and Caco-2 colon cancer cell lines untreated compared with EGF, Cetuximab, Gefitinib,EGF plus Cetuximab and EGF plus gefitinib treatments. Keywords: Gene Expression Profiling
Project description:Transcriptional profiling of HT-29 human colon cancer cells transfected with non-targeting control (NTC) siRNA and two different siRNA sequences against CDK8 (siCDK8-1 and siCDK8-2). Three condition experiment comparing siNTC versus siCDK8-1 and siCDK8-2 after 3 days (3 biological replicates each); in total 9 samples profiled.
Project description:Expression profiling of 29 untreated breast cancer cell lines using Agilent 4x44K V1 (G4112F) dual color oligonucleotide microarrays The primary study objective was to establish a research resource for comparative transcriptomic analysis of a series of commercially available breast cancer cell lines representative of diverse histopathologic and molecular subtypes, generated on the Agilent oligonucleotide platform. A specific study objective was to perform a comparative transcriptional analysis of three cell lines established from a patient with triple negative metaplastic inflammatory breast cancer developed by Drs. Felding Habermann and Smider at the Scripps Research Institute, San Diego, CA. Cancer Res 2011;71(24 Suppl):Abstract nr PD03-07.
Project description:Expression profiling of 29 untreated breast cancer cell lines using Agilent 4x44K V1 (G4112F) dual color oligonucleotide microarrays The primary study objective was to establish a research resource for comparative transcriptomic analysis of a series of commercially available breast cancer cell lines representative of diverse histopathologic and molecular subtypes, generated on the Agilent oligonucleotide platform. A specific study objective was to perform a comparative transcriptional analysis of three cell lines established from a patient with triple negative metaplastic inflammatory breast cancer developed by Drs. Felding Habermann and Smider at the Scripps Research Institute, San Diego, CA. Cancer Res 2011;71(24 Suppl):Abstract nr PD03-07. Commercial cell lines were cultured in replete media using manufacturer-recommended conditions and harvested during exponential growth phase using TRIzol Reagent. Total RNA was prepared from each cell line and a pooled reference was generated containing an equimolar concentration of RNA from all cell lines. Individual cell lines were differentially labeled relative to the reference pool and hybridized to Agilent Commercial V1 4x44K oligonucleotide microarrays.
Project description:Folic acid (FA) is a synthetic form of vitamin B9, generally used as a nutritional supplement and an adjunctive medication in cancer therapy. FA is involved in genetic and epigenetic regulation; therefore, it has a dual modulatory role in established neoplasms. We aimed to investigate the effect of short-term (72 h) FA supplementation on colorectal cancer; hence, HT-29 and SW480 cells were exposed to different FA concentrations (0, 100, 10,000 ng/mL). HT-29 cell proliferation and viability levels elevated after 100 ng/mL but decreased for 10,000 ng/mL FA. Additionally, a significant (p ≤ 0.05) improvement of genomic stability was detected in HT-29 cells with micronucleus scoring and comet assay. Conversely, the FA treatment did not alter these parameters in SW480 samples. RRBS results highlighted that DNA methylation changes were bidirectional in both cells, mainly affecting carcinogenesis-related pathways. Based on the microarray analysis, promoter methylation status was in accordance with FA-induced expression alterations of 27 genes. Our study demonstrates that the FA effect was highly dependent on the cell type, which can be attributed to the distinct molecular background and the different expression of proliferation- and DNA-repair-associated genes (YWHAZ, HES1, STAT3, CCL2). Moreover, new aspects of FA-regulated DNA methylation and consecutive gene expression were revealed.
Project description:DNase-seq on immortalized cell line HT-29, epithelial cells from a 44 year old female adult human colon with a colorectal adenocarcinoma. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf