Cross species hybridization of human cancer cells xenografted into different mouse organ sites
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PROVIDER: PRJNA120607 | ENA |
REPOSITORIES: ENA
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Project description:To test gene expression changes of human cancer cells and mouse surrounding tissue cells during tumor progression, 4 different types of cancer cells (MDA-MB231Br3, PC14Br4, KM12M, A375SM) were injected into mouse brain, skin and orthotopic sites. RNAs containing human cancer cells and mouse surrounding tissue cells were extracted and hybridized into human and mouse arrays at the same times and it revealed the brain microenvironment induced complete reprogramming of metasized cancer cells, resulting in a gain of neuronal cell characteristic , mimicking neurogenesis during development.
2011-09-24 | GSE19184 | GEO
Project description:To test gene expression changes of human cancer cells and mouse surrounding tissue cells during tumor progression, 4 different types of cancer cells (MDA-MB231Br3, PC14Br4, KM12M, A375SM) were injected into mouse brain, skin and orthotopic sites. RNAs containing human cancer cells and mouse surrounding tissue cells were extracted and hybridized into human and mouse arrays at the same times and it revealed the brain microenvironment induced complete reprogramming of metasized cancer cells, resulting in a gain of neuronal cell characteristic , mimicking neurogenesis during development. Human in vivo: 4 KB, 4 KS, 3 KC, 5 MB, 5 MF, 4 MS, 3 PB, 3 PL, 4 PS, 5 AB, 5 AS , 1 BR_N_PC Mouse in vivo: 4 KB, 4 KS, 3 KC, 5 MB, 5 MF, 4 MS, 3 PB, 3 PL, 4 PS, 5 AB, 5 AS , 3 BR, 3 PC_BRM, 1 BR_PCM
2011-09-23 | E-GEOD-19184 | biostudies-arrayexpress
Project description:The objective of this work was to determine the effectiveness of cross-hybridization of gDNA from five native soil nematodes to an Affymetrix Caenorhabditis elegans tiling array. Cross-hybridization experiments using C. briggsae, for which genome information is available, allowed hybridisation intensities to be correlated with known sequence differences. Initial analysis of data by conventional array-based Comparative Genomic Hybridization (aCGH) techniques at the chip level lead to misleading results due to an artefact from the combination of scaling, bandwidth smoothing, and differential GC content in exon and intron regions. To circumvent this artefact, individual probes were instead normalized and centered by adjusting for probe-specific thermodynamic binding affinity. However, cross-hybridization of C. briggsae DNA revealed that the resultant probe intensities alone were still uncorrelated to sequence similarity below 90% identity. Below 90% similarity, all probes hybridize uniformly poorly, and above 90% similarity the hybridization differences are not large enough to detect over background, therefore, no 'threshold' ratio of hybridization intensity was successful at identifying probes with similarity to the heterologous genome. In light of the observations described here, we suggest that the criteria for replication and verification of gene expression profiles generated from cross-species microarray hybridizations be more stringent than typically adopted for con-specific hybridizations.
2010-08-18 | GSE23667 | GEO
Project description:We used two RNA samples that differed only by a set of three hemoglobin transcripts to compare microarray cross-hybridization between two target preparation protocols. We found widespread cross-hybridization using standard cRNA target but substantially less cross-hybridization using cDNA target. Keywords: protocol comparison
2006-09-08 | GSE4532 | GEO
Project description:Array-based cross-species hybridization between genera of Rhabditidae (Nematoda)
| PRJNA130825 | ENA
Project description:The objective of this work was to determine the effectiveness of cross-hybridization of gDNA from five native soil nematodes to an Affymetrix Caenorhabditis elegans tiling array. Cross-hybridization experiments using C. briggsae, for which genome information is available, allowed hybridisation intensities to be correlated with known sequence differences. Initial analysis of data by conventional array-based Comparative Genomic Hybridization (aCGH) techniques at the chip level lead to misleading results due to an artefact from the combination of scaling, bandwidth smoothing, and differential GC content in exon and intron regions. To circumvent this artefact, individual probes were instead normalized and centered by adjusting for probe-specific thermodynamic binding affinity. However, cross-hybridization of C. briggsae DNA revealed that the resultant probe intensities alone were still uncorrelated to sequence similarity below 90% identity. Below 90% similarity, all probes hybridize uniformly poorly, and above 90% similarity the hybridization differences are not large enough to detect over background, therefore, no 'threshold' ratio of hybridization intensity was successful at identifying probes with similarity to the heterologous genome. In light of the observations described here, we suggest that the criteria for replication and verification of gene expression profiles generated from cross-species microarray hybridizations be more stringent than typically adopted for con-specific hybridizations. Genomic DNA from Caenorhabditis elegans N2 (Bristol), C. elegans CB4856 (Hawaiian), C. briggsae AF16, Oscheius tipulae KS585, Oscheius FVV-2 KS555, Mesorhabditis sp. KS587, Acrobeloides sp. KS586, and Chiloplacus sp. KS584 were hybridized onto C. elegans Affymetrix tiling array (two replicate chips were performed for each species).
2010-08-17 | E-GEOD-23667 | biostudies-arrayexpress
Project description:Expression data for a study on cross-species hybridization on single-species microarrays
| PRJNA112793 | ENA
Project description:Abstract Background: One of the approaches for conducting genomics research in organisms that do not yet have a proper microarray template is to profile their expression patterns by using cross-species hybridization (CSH). Several different studies using spotted microarray for CSH resulted with contradicting conclusions as to the ability of CSH to reflect biological processes. Results: We used a tomato spotted cDNA microarray to examine the ability of CSH to reflect species specific hybridization (SSH) data. Potato RNA was hybridized to spotted cDNA tomato and potato microarrays to generate heterologous and homologous hybridization data, respectively. The results revealed difficulties in obtaining transcriptomics data from CSH that reflected those obtained from SSH. Nevertheless, once the data was filtered for those corresponding to matching probe sets, by restricting proper cutoffs of probe homology, the CSH transcriptomics data better reflected those of the SSH, to an extent that was quantitated by identification of differentially regulated genes. Conclusions: This study enabled us to outline some considerations regarding evaluation of a microarray as candidate platform for CSH study, performance of CSH and proper data analysis that may allow CSH to reflect to some extent a biological process. Keywords: cross-species hybridization; heterologous hybridization
2006-05-30 | GSE3584 | GEO
Project description:Interspecies hybridization versus intra-species hybridization for Leishmania promastigote RNA.
| PRJNA104669 | ENA
Project description:In order to study molecular changes in the stroma from tissue samples it is recommended to separate tumor tissue from stromal tissue. This is particularly relevant to mouse tumor xenograft models where tumor, particularly metastatic tumors, can be small and difficult to separate from the host tissue. In our research we compared qualitatively the ability of high-throughput mRNA sequencing, RNA-Seq, and microarrays to detect tumor (human) and stromal (mouse) expression from mixed tumor-stromal samples in terms of the genes and pathways that are involved in cross-alignment (RNA-Seq) and cross-hybridization (microarrays).
2012-12-14 | GSE40890 | GEO