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To identify factors preferentially necessary to drive tumor expansion we performed parallel in vitro and in vivo negative selection shRNA screens. Melanoma cells harboring shRNAs targeting several DNA Damage Response (DDR) kinases had a greater selective disadvantage in vivo than in vitro, indicating an essential contribution of these factors during tumor expansion. In growing tumors, DDR kinases were activated following hypoxia. Correspondingly, depletion or pharmacologic inhibition of DDR kinases was toxic to melanoma cells, including those that were resistant to BRAF inhibitor, and this could be enhanced by angiogenesis blockade. These results reveal that hypoxia sensitizes melanomas to targeted inhibition of the DDR and illustrate the utility of in vivo shRNA dropout screens for identification of pharmacologically tractable targets. A lentivirus-based kinome shRNA library (four pools) was used to transduce 888mel cells (MOI<0.2). After puromycin selection (1μg/ml), two reference samples were collected as controls. Next, tumor cells (5x105 per injection) were either injected s.c. into 6 NSG mice or plated into 6 independent plates (5x105) for in vitro culture. Tumors were removed from the mice and genomic DNA used to recover shRNAs by PCR amplification followed by deep sequencing. Three analyses were performed independently in parallel: (1) Tumors versus cultured cells (Log2 Fold Change < -1); (2) Tumors versus references (Log2 Fold Change < -2.5) and (3) Cultured cells versus references (Log2 Fold Change < -2.5). Genes targeted with at least 2 shRNAs in each of the analysis were considered hits with an enhanced in vivo effect.
Data Types:
  • Other
Dendritic Cell differentiation - CD molecule cluster follow up: The data files associated to this experiment show the gene expression levels for a subset of 152 transcripts (out of 12626 genes represented on Affymetrix Genechip HG_U95Av2) representing CD molecules specifically expressed in Dendritic Cells (DC) as assessed by the 9 conditions tested. Another subset of genes, corresponding to a cluster of Transcription regulators is available from E-MEXP-2 experiment.
Data Types:
  • Software/Code
  • Tabular Data
  • Text
  • File Set
Gene transcription profiling in liver following high fat versus normal diet in C57/Bl6 mice. Characterisation of molecular mechanisms of in vivo insulin action in mouse models of experimentally induced Insulin Resistance. Switched the diet after mice are 5 weeks old, then sampled at 8 days, 3 weeks and 15 weeks.
Data Types:
  • Software/Code
  • Geospatial Data
  • Image
  • Tabular Data
  • Text
  • File Set
PAO1 was grown in sub-inhibitory ciprofloxacin (0.1x-, 0.3x-, 1x-MIC) until log phase. Microarrays were done on total RNA isolated from these cultures. Loop design and dye swapping were used.
Data Types:
  • Software/Code
  • Geospatial Data
  • Image
  • Tabular Data
  • Text
Mice which lack IRS-2, develop insulin resistance. Comparison between white adipose tissue from 5 week old IRS-2 KO and wild type mice. Processed data is not included for this experiment and therefore these data are not MIAME compliant
Data Types:
  • Software/Code
  • Geospatial Data
  • Image
  • Tabular Data
  • Text
Study comprising 74 kidney tumor samples of different histological type, differentiation grade, stage and with data on chromosomal aberrations and follow-up. Samples were hybridised against a common reference obtained from pooling different kidney tumor samples.
Data Types:
  • Software/Code
  • Geospatial Data
  • Image
  • Tabular Data
  • Text
  • File Set
Gene transcription profiling in muscle following muscle versus normal diet in C57/Bl6 mice. Switched the diet when mice were 5 weeks old, then sampled at 8 days, 3 weeks and 15 weeks.
Data Types:
  • Software/Code
  • Geospatial Data
  • Image
  • Tabular Data
  • Text
  • File Set
Gene transcription profiling in Epidydimal fat pad (EPD) following High fat versus normal diet in C57/Bl6 mice. Characterisation of molecular mechanisms of in vivo insulin action in mouse models of experimentally induced Insulin resistance. Switched the diet when mice were 5 weeks old, then sampled at 8 days.
Data Types:
  • Software/Code
  • Geospatial Data
  • Image
  • Tabular Data
  • Text
  • File Set
Finally differentiated 3T3-L1 adipocytes are treated with insulin (0 or 100nM)or metformin (0 or 2mM)for 2 and 12 hours to understand insulin and metformin(an anti-diabetic drug commonly applied for Non-Insulin Dependent Diabetes Mellitus)action in adipose tissues.
Data Types:
  • Software/Code
  • Geospatial Data
  • Image
  • Tabular Data
  • Text
Gene transcription profiling in Epidydimal fat pad (EPD) following High fat versus normal diet in C57/Bl6 mice. The diet was switched when mice were 5 weeks old, then samples taken at 2 days, 8 days, 3 weeks and 15 weeks.
Data Types:
  • Software/Code
  • Geospatial Data
  • Image
  • Tabular Data
  • Text
  • File Set