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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from Pax7+ satellite cell derived tumors in vitro and in vivo

ABSTRACT: Mouse muscle stem cells, defined as Pax7+ satellite cells, can initiate rhabdomyosarcoma when transformed by oncogenic Kras and concomitant loss of p53. Mouse Pax7+ satellite cells were transformed in vitro and in vivo utilizing the Cre-ER/loxp system. We wanted to address two major questions: do the in vitro and in vivo tumors cluster together compared to another mouse to another mouse derived soft-tissue sarcoma AND which human soft-tissue sarcoma do the in vivo derived tumors resemble transcriptionally? Therefore, tumors from cells transformed in vitro and tumors from mice that restrict the oncogenic lesions to Pax7+ satellite cells in vivo were compared to answer these two questions.

ORGANISM(S): Mus musculus

SUBMITTER: Jordan Blum

PROVIDER: E-GEOD-22798 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from Pax7+ satellite cell derived tumors in vitro and in vivo

Project description:Mouse muscle stem cells, defined as Pax7+ satellite cells, can initiate rhabdomyosarcoma when transformed by oncogenic Kras and concomitant loss of p53. Mouse Pax7+ satellite cells were transformed in vitro and in vivo utilizing the Cre-ER/loxp system.

2011-06-01 | GSE22798 | GEO

Undifferentiated Pleomorphic Sarcoma Model

Project description:Analysis of undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma-like tumors from LSL-KrasG12D, p53Fl/Fl mouse model of soft tissue sarcoma. Murine soft tissue sarcomas (n = 17) were compared to normal muscle (n = 4). Tumors were isolated surgically from soft tissue sarcomas generated by conditional Kras and p53 alleles. Tumors were induced using an adenovirus expressing Cre recombinase. Normal muscle samples were isolated from mice of the same genotype without tumor induction.

2010-03-03 | E-GEOD-16779 | biostudies-arrayexpress

Discrete subsets of myogenic and mesenchymal precursors give rise to soft tissue sarcomas of distinct lineage differentiation

Project description:This work examines sarcoma formation within discrete subsets of KRAS(G12V)-expressing p16p19null myogenic and mesenchymal cells found normally in skeletal muscle. We show that prospectively isolated skeletal muscle precursor cells (SMPs) within the satellite cell pool can serve as cancer cells-of-origin for mouse rhabdomyosarcomas (soft tissue sarcomas with features of myogenic differentiation). Alternatively, non-myogenic progenitors (ScaPCs) induce sarcomas lacking myogenic differentiation markers. We used Affymetrix whole mouse genome 430 2.0 microarrays to gain deeper insights into the molecular underpinnings of the three types of KRAS; p16p19null mouse soft-tissue sarcomas (originating from SMPs, ScaPCs and CD45-MAC1-TER119-Sca1-CXCR4- cells). Four replicates of each type.

2011-11-10 | E-GEOD-22841 | biostudies-arrayexpress

Undifferentiated Pleomorphic Sarcoma Model Using Tumors from BrafCa

Project description:Analysis of undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma like tumors from BrafCa, p53Fl/Fl mouse model of soft tissue sarcoma

2014-12-01 | GSE20049 | GEO

Undifferentiated Pleomorphic Sarcoma Model

Project description:Analysis of undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma-like tumors from LSL-KrasG12D, p53Fl/Fl mouse model of soft tissue sarcoma.

2009-11-21 | GSE16779 | GEO

Transcription profiling of synovial sarcoma-like tumors induced in a genetically engineered mouse model

Project description:Synovial sarcoma-like tumors were generated in mice by conditionally expressing the human t(X;18) translocation-derived SYT-SSX2 fusion protein. Using a Tamoxifen-inducible CreER system, we show here that sporadic expression of SYT-SSX2 across multiple tissue types leads to exclusive formation of synovial sarcoma-like tumors while its widespread expression is lethal. CreER-based sporadic expression both avoids the severe early developmental phenotypes associated with widespread SYT-SSX2 expression and better models natural pathogenesis of cancers where transformed cells usually arise within an environment of largely normal cells. Experiment Overall Design: Genetically engineered mice capable of conditionally expressing the human synovial sarcoma-associated SYT-SSX2 fusion oncogene were mated with genetically engineered mice expressing the CreER fusion protein from ROSA locus. The progenies harboring both CreER and SYT-SSX2 were followed up with or without tamoxifen injection. Tumors were generated in these mice that were dissected out, RNA extracted, and subjected to expression profiling by microarray analysis.

2009-04-24 | E-GEOD-14469 | biostudies-arrayexpress

Mus musculus

Project description:Expression data from Pax7+ satellite cell derived tumors in vitro and in vivo

| PRJNA127825 | ENA

Clear cell sarcoma human HEEBO microarray data

Project description:Clear cell sarcoma (CCS) of tendons and aponeuroses is a deadly soft-tissue malignancy resembling melanoma, with a predilection for young adults. EWS-ATF1, the fusion product of a balanced chromosomal translocation between chromosomes 22 and 12, is considered the definitional feature of the tumor. Conditional expression of the EWS-ATF1 human cDNA in the mouse generates CCS-like tumors with 100 percent penetrance. Tumors, developed through varied means of initiating expression of the fusion oncogene, model human CCS morphologically, immunohistochemically, and by genome-wide expression profiling. We also demonstrate that while fusion oncogene expression in later stages of differentiation can transform mesenchymal progenitor cells and generate tumors resembling CCS generally, expression in cells retaining stem cell markers permits the full melanoma-related phenotype. Nielsen et al. ("Molecular characterisation of soft tissue tumours: a gene expression study"; PMID 11965276) used microarray to compare a variety of soft-tissue neoplasms morphologically similar to clear cell sarcoma. In our study, we use their expression data (not previously submitted) in the profiling of our mouse mutant that models clear cell sarcoma. The mRNA profiles of a variety of soft-tissue neoplasm samples are examined by HEEBO microarrays. Included here are a total of 6 different types of tumors, and 5 of them have at least one biological replicate. The authors of "Molecular characterisation of soft tissue tumours: a gene expression study" (PMID 11965276) performed these microarray experiments, including data processing and normalization. We obtained these expression data, and used them to train a support vector machine, which was later used to characterize our mouse model of clear cell sarcoma (data submitted elsewhere).

2012-12-20 | E-GEOD-43045 | biostudies-arrayexpress

Proliferation and Tumorigenesis of a Murine Sarcoma Cell Line in the Absence of Dicer

Project description:MicroRNAs are a class of short ~22 nucleotide RNAs predicted to regulate nearly half of all protein-coding genes, including many involved in basal cellular processes and organismal development. Although both increases and decreases in the levels of specific miRNAs have been shown to promote tumor development, a global reduction in miRNAs is commonly observed in various human tumors. However, complete loss has not been documented, suggesting an essential function for miRNAs in tumorigenesis. Here we present the finding that transformed or immortalized Dicer-null somatic cells can be isolated readily in vitro, maintain the characteristics of Dicer-expressing controls and remain stably proliferative. Furthermore, Dicer-null cells from a sarcoma cell line, though depleted of miRNAs, are competent for tumor formation. Hence, miRNA levels in cancer may be maintained in vivo by a complex stabilizing selection in the intratumoral environment. Small RNAs from tumor cell lines (murine sarcoma KrasG12D, p53 -/-) with and without Dicer (Dicer f/-, Dicer -/-) were analyzed.

2012-08-20 | E-GEOD-34825 | biostudies-arrayexpress

Subtype-specific genomic alterations define new targets for soft tissue sarcoma therapy

Project description:This SuperSeries is composed of the following subset Series: GSE21122: Whole-transcript expression data for soft-tissue sarcoma tumors and control normal fat specimens GSE21123: Affymetrix SNP array data for soft tissue sarcoma samples Refer to individual Series

2010-07-05 | E-GEOD-21124 | biostudies-arrayexpress

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