Transcriptional profiling of a breast cancer cell line panel using RNAseq technology
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Heiser Laura
PROVIDER: S-ECPF-GEOD-48213 | biostudies-other |
REPOSITORIES: biostudies-other
Similar Datasets
Project description:56 breast cancer cell lines were profiled to identify patterns of gene expression associated with subtype and response to therapeutic compounds.
2013-08-20 | GSE48213 | GEO
Project description:56 breast cancer cell lines were profiled to identify patterns of gene expression associated with subtype and response to therapeutic compounds. Cell lines were profiled in their baseline, unperturbed state.
2013-08-20 | E-GEOD-48213 | biostudies-arrayexpress
Project description:In an experimental model of tumor dormancy, heat shock protein 27 (HSP27) was up-regulated in angiogenic human breast cancer cells when compared with non-angiogenic cells. Stable down-regulation of HSP27 in angiogenic tumor cells was followed by long-term tumor dormancy in vivo and associated with reduced intra-tumoral endothelial cell proliferation, decreased secretion of VEGF and bFGF from tumor cells, and increased expression of thrombospondin-1. Phosphorylation of the transcription factor STAT3 and nuclear expression of NFκB were reduced following suppression of HSP27. In contrast, tumor cell proliferation and apoptosis were not affected. By clinical validation, high HSP27 expression was associated with markers of aggressive tumors and decreased survival in breast cancer and melanoma patients. Our present findings suggest a link between HSP27 and dormancy through tumor-vascular interactions. Targeting HSP27, a multifunctional cytoprotective protein, might offer a novel strategy in cancer treatment.
| S-ECPF-TABM-883 | biostudies-other
Project description:Long non-coding RNAs (lncRNAs) form a new class of RNA molecules implicated in various aspects of protein coding gene expression regulation. To study lncRNAs in cancer, we generated expression profiles for 1707 human lncRNAs in the NCI60 cancer cell line panel using a high-throughput nanowell RT-qPCR platform. We describe how qPCR assays were designed and validated and provide processed and normalized expression data for further analysis. Data quality is demonstrated by matching the lncRNA expression profiles with phenotypic and genomic characteristics of the cancer cell lines. This data set can be integrated with publicly available omics and pharmacological data sets to uncover novel associations between lncRNA expression and mRNA expression, miRNA expression, DNA copy number, protein coding gene mutation status or drug response.
| S-EPMC4932877 | biostudies-literature
Project description:A panel of twelve breast cancer cell lines (ATCC) were exposed to 0, 1 or 10 nM 17β-estradiol (E2) for 16 hours. Cells were maintained in DMEM/F12 1:1 (DF) supplemented with 10% or 20% fetal calf serum (FCS) or 20% FCS and 0.01 mg/ml insulin. Two days before experiments, cells were seeded in 60 mm plates in DF with charcoal stripped phenol red-free serum supplemented with non-essential amino-acids and pen/strep, at a density such that 75%-90% confluence was obtained by the time of harvesting. Medium was refreshed 24 hours before exposure to 1 nM E2, 10 nM E2 or DMSO (control) for 16h. Subsequently cells were harvested and RNA was extracted using the Nucleospin RNA isolation kit (Macherey-Nagel).
2019-06-01 | GSE127760 | GEO
Project description:To better characterize group IE like human breast cancer based on the gene profiles of estrogen actions through estrogen receptor alpha (ER alpha), we identified an ER alpha transcriptional regulatory network for cell cycle in silico. We used two datasets from cell line (Data 1) and clinical samples (Data 2), respectively. Analyses on Data 1 via trajectory clustering and Pathway-Express confirmed the significant estrogen effect on up-regulating cell cycle activities. The gene expression relationships between ER alpha and cell cycle genes were re-identified in Data 2 by three statistical methods – Galton-Pearson’s correlation coefficient, Student’s t-test and the coefficient of intrinsic dependence. They were mostly (56.09%)(46/82) re-confirmed by literature search. E2F1 was found to be the major ER alpha target in regulating cell cycle gene expressions (83.72%)(36/43) via suppressive mode. However, enhanced cell cycle progression via up-regulating some cell cycle genes was predicted in silico possibly involving E2F2, in part. Both tumorigenic and tumor suppressing activities indicated by this network were predicted. This network clearly provides a robust way for uncovering estrogen actions in an ER(+) subtype specific manner. Experiment Overall Design: Two clinical datasets were used in this study. One, the 37 clinical arrays (abbreviated as 37A) consist of 26 A for patients positive in estrogen receptor alpha (ER) and in progesterone receptor (PR) immunohistochemical stain (IHC) and 11A for patients negative in ER IHC. This dataset was designated as Data 2. The 31 clinical arrays (31A) consist of 20A for patients positive in ER status but negative in PR status and 11A which are the same as in 37A. This dataset was used for data comparison. All the signals from the mRNA profile of each sample in the experiments were normalized using the internal control RNA- Stratagene's human common reference RNA via statistical method 'rank consistant lowess. Finally, those ratios were transformed by Log2.
| S-ECPF-GEOD-17040 | biostudies-other
Project description:Total RNA from 128 primary breast tumors was labelled using the Illumina TotalPrep RNA Amplification kit (Ambion) following manufacturers instructions. 1.5 ug of biotin-labelled cRNA were used for each hybridisation on Sentrix Human-6 BeadChips v1.0 (Illumina, San Diego, CA) following manufacturers protocol.
| S-ECPF-TABM-576 | biostudies-other
Project description:E. coli is the main causative agent of mastitis in dairy cows, but the mechanism of molecular regulation underlying the occurrence and development of mastitis has not yet been fully elucidated. In this study, an E. coli-induced mastitis model was created and RNASeq technology was used to measure the miRNA expression profiles at different times post-infection (0, 1, 3, 5, 7 dpi), as well as to screen for differentially expressed miRNA. The results show detection of 2416 miRNAs, including 628 known miRNAs and 1788 newly discovered miRNAs. A total of 200 differentially expressed miRNAs were found at different time points. Bioinformatics analysis showed that these differentially expressed miRNAs may regulate the occurrence and development of mastitis in dairy cows through seven signal transduction pathways, namely cytokine-cytokine receptor interaction, MAPK signaling pathway, chemokine signaling pathway, leukocyte transendothelial migration, T cell receptor signaling pathway, Toll-like receptor signaling pathway, and cell adhesion molecules. In addition, bta-miR-200a, bta-miR-205, bta-miR-122, bta-miR-182 and the newly discovered conservative_15_7229 might be involved in immune process in late stage of E. coli-induced mastitis. The results of this study lay the foundation for molecular network analysis of mastitis and molecular breeding of dairy cows.
| S-EPMC6107498 | biostudies-other
Project description:Breast cancer cell line panel stimulated with estradiol
| PRJNA525306 | ENA
Project description:Sugarcane smut disease is caused by the biotrophic fungus Sporisorium scitamineum. The disease is characterized by the development of a whip-like structure from the primary meristems, where billions of teliospores are produced. Sugarcane smut also causes tillering and low sucrose and high fiber contents, reducing cane productivity. We investigated the biological events contributing to disease symptoms in a smut intermediate-resistant sugarcane genotype by examining the transcriptional profiles (RNAseq) shortly after inoculating the plants and immediately after whip emission. The overall picture of disease progression suggests that premature transcriptional reprogramming of the shoot meristem functions continues until the emergence of the whip. The guidance of this altered pattern is potentially primarily related to auxin mobilization in addition to the involvement of other hormonal imbalances. The consequences associated with whip emission are the modulation of typical meristematic functions toward reproductive organ differentiation, requiring strong changes in carbon partitioning and energy production. These changes include the overexpression of genes coding for invertases and trehalose-6P synthase, as well as other enzymes from key metabolic pathways, such as from lignin biosynthesis. This is the first report describing changes in the transcriptional profiles following whip development, providing a hypothetical model and candidate genes to further study sugarcane smut disease progression.
| S-EPMC5008620 | biostudies-literature