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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Primary Mammary Epithelial Cells: Control vs 1023-Treated

ABSTRACT: Gene expression profiling of primary mammary epithelial cells treated for 72 hours with compound 1023 compared to DMSO. Goal was to determine genes differntially regulated by treatment with the novel compound, 1023. Two-condition experiment, DMSO vs. 1023. Biological replicates: 2 control replicates, 2 1023 replicates.

ORGANISM(S): Mus musculus

SUBMITTER: Bryan Welm

PROVIDER: E-GEOD-39249 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Chemical genetic screen reveals a role for desmosomal adhesion in mammary branching morphogenesis.

Basham Kaitlin J KJ Kieffer Collin C Shelton Dawne N DN Leonard Christopher J CJ Bhonde Vasudev R VR Vankayalapati Hariprasad H Milash Brett B Bearss David J DJ Bearss David J DJ Looper Ryan E RE Welm Bryan E BE

The Journal of biological chemistry 20121203 4

During the process of branching morphogenesis, the mammary gland undergoes distinct phases of remodeling to form an elaborate ductal network that ultimately produces and delivers milk to newborn animals. These developmental events rely on tight regulation of critical cellular pathways, many of which are probably disrupted during initiation and progression of breast cancer. Transgenic mouse and in vitro organoid models previously identified growth factor signaling as a key regulator of mammary br ...[more]

PMID: 23212921

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Primary Mammary Epithelial Cells: Control vs 1023-Treated

Project description:Gene expression profiling of primary mammary epithelial cells treated for 72 hours with compound 1023 compared to DMSO. Goal was to determine genes differntially regulated by treatment with the novel compound, 1023.

2012-12-31 | GSE39249 | GEO

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Transformation of enriched mammary cell populations with Polyoma Middle T Antigen influences tumor subtype and metastatic potential

Project description:Breast cancer is a multifaceted disease, exhibiting significant molecular, histological, and pathological diversity. Factors that impact this heterogeneity are poorly understood; however, transformation of distinct normal cell populations of the breast may generate different tumor phenotypes. Our previous study demonstrates that the polyomavirus middle T antigen (PyMT) oncogene can establish diverse tumor subtypes when broadly expressed within mouse mammary epithelial cells. Herein, we assess the molecular, histological, and metastatic outcomes from distinct mammary cell populations transformed with PyMT. By combining several methodologies, including lentiviral infection, cell sorting, and transplantation, we have characterized tumors arising from enriched populations of mammary epithelial cells. We have found that expression of PyMT within different cell populations influences tumor histology, molecular subtype, and metastatic potential. 32 samples, 1 from each of 32 mouse mammary tumors arising from transplanted mouse mamary epithelial cells (MMECs) transduced with PyMT-expressing lentivirus. MMECs were sorted into four different types prior to transplant: luminal CD133+ (8 samples), luminal CD133- (11 samples), stem (6 samples), and basal (7 samples). The background for the cell donor and transplant recipients mice was FVB/NJ obtained from Jackson Laboratories.

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Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.): custom genetic tools for exploring herbivore ecology

Project description:We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) with the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). To compare the effect of native diet/habitat and phylogenetic similarity, we performed 3 experiments with the Neotoma probes only: one across species with similar habitat niches (N. lepida versus N. bryanti, Palm Springs), one across species with different habitat niches (N. lepida versus N. bryanti, Caspers Wilderness), and one across populations within a species (N. bryant Palm Springs versus Caspers Wilderness). The resulting one-color arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). Biotransformation processes and functions were highly represented in the results. Comparisons between ecologically similar woodrat species revealed fewer gene expression differences than ecologically different woodrat species. The conspecific comparison had overall fewest differences. Gene expression was compared across 3 groups of woodrats: Neotoma lepida (n=4), N. bryanti Palm Springs (n=4), and N. bryanti Caspers Wilderness (n=4). Animals were fed a rabbit chow diet, called control; intake was monitored over 10 days, after which RNA was extracted from hepatic tissue. One-color arrays were performed.

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Aflatoxin B1 exposure induces epigenetic mechanisms in primary human hepatocytes revealing novel biological processes associated with hepatocellular carcinoma (miRNA)

Project description:The study investigated differential gene expression, microRNA expression and DNA methylation changes in a pool of primary human hepatocyte RNA and DNA following 5 days of repetitive exposure to a low or moderate dose of aflatoxin B1 or DMSO. Three biological replicates per compound/solvent.

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Aflatoxin B1 exposure induces epigenetic mechanisms in primary human hepatocytes revealing novel biological processes associated with hepatocellular carcinoma (Affymetrix)

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The gene expression changes by CID 70698683

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