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TranscriptomicsQuantification of Normal Cell Fraction and Copy Number Neutral LOH in Clinical Lung Cancer Samples Using SNP Array Data
Technologies based on DNA microarrays have the potential to provide detailed information on genomic aberrations in tumor cells. In practice a major obstacle for quantitative detection of aberrations is the heterogeneity of clinical tumor tissue. Tumor tissue consists of a mixture of tumor cells and ...
ORGANISM(S): Homo sapiens 
2010-04-09 | E-GEOD-16092 | biostudies-arrayexpress
TranscriptomicsCharacterization of the RNA content of chromatin
We deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harbouring CARS. We purified CARs from normal HFs by isolating soluble chromatin after MNase treatment, followed by separation of...
ORGANISM(S): Homo sapiens 
2010-04-13 | E-GEOD-21227 | biostudies-arrayexpress
TranscriptomicsAffymetrix SNP array data for Chronic Lymphocytic Leukemia_diagnostic sample_patient samples
High-resolution genomic microarrays provides simultaneous detection of copy-number aberrations such as the known recurrent aberrations in Chronic Lymphocytic Leukemia_diagnostic sample_patient (del(11q), del(13q), del(17p) and trisomy 12), and copy-number neutral loss of heterozygosity. We screened...
ORGANISM(S): Homo sapiens 
2011-04-28 | E-GEOD-28030 | biostudies-arrayexpress
TranscriptomicsCD99 is a novel prognostic stromal marker in non-small cell lung cancer
The delicate interaction between cancer cells and the surrounding stroma plays an essential role in all stages of tumourigenesis. Despite the significance of this interplay, alterations in protein composition underlying tumour-stroma interactions are largely unknown. The aim of this study was to ide...
ORGANISM(S): Homo sapiens 
2012-06-05 | E-GEOD-33363 | biostudies-arrayexpress
TranscriptomicsGene Copy Number Aberrations are Associated with Survival in Histological Subgroups of Non-Small Cell Lung Cancer
This SuperSeries is composed of the following subset Series: GSE28571: Gene Copy Number Aberrations are Associated with Survival in Histological Subgroups of Non-Small Cell Lung Cancer (expression data) GSE28572: Gene Copy Number Aberrations are Associated with Survival in Histological Subgroups of ...
ORGANISM(S): Homo sapiens 
2011-11-01 | E-GEOD-28582 | biostudies-arrayexpress
TranscriptomicsScreening for copy-number alterations and LOH in CLL - a comparative study of four microarray platforms
Screening for gene copy-number alterations (CNAs) has improved by applying genome-wide microarrays, where SNP arrays also allow analysis of loss of heterozygozity (LOH). We here analyzed 10 chronic lymphocytic leukemia (CLL) samples using four different high-resolution platforms: BAC arrays (32K), o...
ORGANISM(S): Homo sapiens 
2008-12-10 | E-GEOD-13557 | biostudies-arrayexpress
TranscriptomicsGene Copy Number Aberrations are Associated with Survival in Histological Subgroups of Non-Small Cell Lung Cancer (copy number data)
Hypothesis: Non-small cell lung cancer (NSCLC) is characterized by a multitude of genetic aberrations with unknown clinical impact. In this study, we aimed to identify gene copy number changes that correlate with clinical outcome in NSCLC. To maximize the chance to identify clinically relevant event...
ORGANISM(S): Homo sapiens 
2011-11-01 | E-GEOD-28572 | biostudies-arrayexpress
TranscriptomicsExpression data from hypervitaminosis A rat diaphyseal bone
Vitamin A is the only known compound that produces spontaneous fractures in rats. In an effort to resolve the molecular mechanism behind this effect, we fed young rats high doses of vitamin A and performed a global transcriptional analysis of diaphyseal bone after one week, i.e. just before the firs...
ORGANISM(S): Rattus norvegicus 
2011-12-21 | E-GEOD-29859 | biostudies-arrayexpress
TranscriptomicsSNP array analysis of lung cancer NCI-H1395, diluted to different tumor cell concentrations
In vitro mix of DNA from patient-matched lung cancer and blood cell lines, representing 30,50,70,100% tumor cell tissue, analyzed on Affymetrix 6.0 arrays. Lung cancer cell line H-1395 and patient-matched blood cell line BL1395 were obtained from ATCC and cultured according to their recommendations....
ORGANISM(S): Homo sapiens 
2011-09-08 | E-GEOD-29172 | biostudies-arrayexpress
TranscriptomicsGene Copy Number Aberrations are Associated with Survival in Histological Subgroups of Non-Small Cell Lung Cancer (expression data)
Hypothesis: Non-small cell lung cancer (NSCLC) is characterized by a multitude of genetic aberrations with unknown clinical impact. In this study, we aimed to identify gene copy number changes that correlate with clinical outcome in NSCLC. To maximize the chance to identify clinically relevant event...
ORGANISM(S): Homo sapiens 
2011-10-27 | E-GEOD-28571 | biostudies-arrayexpress
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