Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Melanoma Cells Grown in Stem Cell Media

ABSTRACT: Cells from patient melanoma samples were grown de novo in either a stem cell media (SCM) or in standard serum containing media, as well as xenografts derived from each culture type. The expression profile of these samples were compaired to the expression profile of the original patient tumour sample.

ORGANISM(S): Homo sapiens

SUBMITTER: Matthew Anaka

PROVIDER: E-MEXP-3290 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The Ludwig Institute for Cancer Research Melbourne Melanoma Cell Line Panel

Project description:Expression profiling of a panel of metastatic melanoma cell lines

2013-02-01 | E-MTAB-1496 | biostudies-arrayexpress

Clonal heterogeneity in melanoma

Project description:Genetic heterogeneity is an important feature of solid tumors, however it is often assumed that most cancer cell lines are genetically homogeneous. A disparity in genetic complexity between cell lines and the disease they model could result in problems such as in vitro preclinical experiments overstating the effectiveness of putative therapeutics. We therefore derived clonal sublines by single cell cloning of in house derived early passage melanoma cell lines (LM-MEL-series), and compared their genomes to each other and the parental cell line using Illumina 610-Quad SNP arrays.

2013-09-08 | E-MTAB-1753 | biostudies-arrayexpress

Transcription profiling by array of human Acute Lymphobastic Leukemia xenografts in mouse to validate the mouse model

Project description:Pre-clinical models that effectively recapitulate human disease are critical for expanding our knowledge of cancer biology and drug resistance mechanisms. For haematological malignancies, the non-obese diabetic/severe combined immunodeficient (NOD/SCID) mouse is one of the most successful models to study paediatric acute lymphoblastic leukaemia (ALL). However, for this model to be effective for studying engraftment and therapy responses at the whole genome level, careful molecular characterisation is essential.Here, we sought to validate species-specific gene expression profiling in the high engraftment continuous ALL NOD/SCID xenograft. Using the human Affymetrix whole transcript platform we analysed transcriptional profiles from engrafted tissues without prior cell separation of mouse cells and found it to return highly reproducible profiles in xenografts from individual mice. The model was further tested with experimental mixtures of human and mouse cells, demonstrating that the presence of mouse cells does not significantly skew expression profiles when xenografts contain 90% or more human cells. In addition, we present a novel in silico and experimental masking approach to identify probes and transcript clusters susceptible to cross-species hybridisation.We demonstrate species-specific transcriptional profiles can be obtained from xenografts when high levels of engraftment are achieved or with the application of transcript cluster masks. Importantly, this masking approach can be applied and adapted to other xenograft models where human tissue infiltration is lower. This model provides a powerful platform for identifying genes and pathways associated with ALL disease progression and response to therapy in vivo.

2010-04-26 | E-MEXP-2648 | biostudies-arrayexpress

Analysis of glioblastoma tumor cell-specific gene expression profiles of distinct histological phenotypes

Project description:Here, we analyzed patient-derived glioblastoma xenografts generated in the mouse brain that give rise to three different histological phenotypes: (i) a highly invasive phenotype (ii) a highly angiogenic phenotype and (iii) an intermediate phenotype. Cell type-specific transcriptomic profiles of tumor and stromal endothelial cells were analyzed to reveal phenotype-specific gene expression patterns and the reciprocal crosstalk between tumor and stromal endothelial cells. This part of the study contains the analysis of the stromal endothelial cells of the host mice. The analysis of the patient-derived tumor cells is found under E-MTAB-3948.

2016-06-30 | E-MTAB-3949 | biostudies-arrayexpress

Transcription profiling of human CD133 positive and negative colon cancer cells

Project description:CD133+ VS CD133-

2010-11-01 | E-MEXP-2467 | biostudies-arrayexpress

Transcriptional effects of lentiviral vector-mediated PDK1 gene silencing in ovarian cancer xenografts

Project description:This experiment was designed to investigate the effect of PDK1 silencing on tumor growth, metabolism, and microenvironment modulation in vivo. Tumors were established in NOD/SCID mice by subcutaneous (s.c.) injection of an highly glycolytic ovarian cancer cell line (OVCAR3) transduced with lentiviral vectors encoding PDK1-specific shRNA and selected in puromycin-containing medium. These cells had >70% reduced expression of PDK1 protein in vitro. OVCAR3 cells transduced with a scrambled shRNA lentiviral vector were used as control. Total RNA was extracted from tumor samples and hybridized on Affymetrix GeneChip™ PrimeView™ Human Gene Expression Arrays. Transcriptome analysis was performed with RNA purified from 5 different tumor samples per group (n=5 mice/shRNA and n=5 mice/shPDHK1), obtained from different mice sacrificed at equivalent tumor volumes (200 mm3).

2020-12-31 | E-MTAB-9877 | biostudies-arrayexpress

Secretome identification of immune cell factors mediating metastatic cell homing

Project description:Metastatic cell homing is a complex process mediated in part by diffusible factors secreted from immune cells found at a pre-metastatic niche. We report on connecting together secretomics and a TRanscriptional Activity CEll aRray (TRACER) to identify functional paracrine interactions between immune cells and metastatic cells as novel mediators of metastatic cell homing. Splenocytes from orthotopic mouse models of breast cancer were isolated to generate a diseased splenocyte conditioned media (D-SCM) containing immune cell secreted factors. MDA-MB-231 metastatic cell activity including cell invasion, migration, transendothelial migration, and proliferation were increased when cultured with D-SCM compared to healthy SCM (H-SCM) and unconditioned media controls. Our secretome analysis of D-SCM yielded secreted factor candidates that contribute to increased metastatic cell activity. In parallel, we identified active TFs within metastatic cells in response to the secreted factors using TRACER. We connected both data sets using MetaCore software to determine interactions between immune cell secreted factors and active metastatic cell TFs to narrow down functional secreted factor candidates that mediate metastatic cell homing. Haptoglobin was among the list of secreted factors and was validated in vitro as a key mediator of metastatic cell recruitment. Furthermore, we designed an implantable poly(lactide-co-glycolide) biomaterial scaffold as a mimic of the pre-metastatic niche to slowly release haptoglobin and demonstrate increased homing of metastatic cells to the scaffold in vivo. Taken together, our studies demonstrate a novel systems biology technique to identify functional paracrine signaling factors, which were validated to reveal mediators of metastatic cell homing.

2015-12-17 | PXD002051 | Pride

Analysis of glioblastoma tumor cell-specific gene expression profiles of distinct histological phenotypes

Project description:Here, we analyzed patient-derived glioblastoma xenografts generated in the mouse brain that give rise to three different histological phenotypes: (i) a highly invasive phenotype (ii) a highly angiogenic phenotype and (iii) an intermediate phenotype. Cell type-specific transcriptomic profiles of tumor and stromal endothelial cells were analyzed to reveal phenotype-specific gene expression patterns and the reciprocal crosstalk between tumor and stromal endothelial cells. This part of the study contains the analysis of the patient-derived tumor cells. The analysis of the stromal endothelial cells of the host mice is found under E-MTAB-3949.

2016-06-30 | E-MTAB-3948 | biostudies-arrayexpress

Pharmacological inhibition of TREM1 attenuates patient derived xenograft models

Project description:To characterize the transcriptional changes in PDX tumors during TREM1 inhibition by microarray

2023-09-27 | E-MTAB-13257 | biostudies-arrayexpress

A Pre-clinical model of induction therapy and relapse in pediatric acute lymphoblastic leukemia

Project description:Relapse and acquired drug resistance in T-cell acute lymphoblastic leukemia (T-ALL) remains a significant clinical problem. The current study used a pre-clinical model of induction therapy for pediatric ALL in NOD/SCID mice (Samuels et al Blood Cancer Journal (2014) 4, e232; doi:10.1038/bcj.2014.52) to study the development of drug resistance. We performed transcription profiling by array of human CD45-positive lymphocytes from patients with acute pediatric lymphoblastic leukemia, xenografted in NOD/SCID mice treated with vincristine, daunorubicin, dexamethasone and L-asparagine. Both the primary-patient-derived and xenograft cells were analysed. The VLXD2 treatment regime is described in full in the protocols associated with this submission and in Samuels et al (Blood Cancer Journal (2014) 4, e232; doi:10.1038/bcj.2014.52). This study is an extension of E-MEXP-3916.

2017-05-01 | E-MTAB-4759 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data