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TranscriptomicsComparative genomic hybridization of human lymph node tumor samples to calculate absolute DNA copy numbers
Array CGH data were used to achieve absolute DNA copy numbers
ORGANISM(S): Homo sapiens 
2008-11-20 | E-TABM-399 | biostudies-arrayexpress
TranscriptomicsWidespread, focal copy number variations (CNV) in Trypanosoma cruzi strains
Trypanosoma cruzi is a protozoan parasite and the etiologic agent of Chagas disease, an important public health problem in Latin America. T. cruzi is diploid, almost exclusively asexual, and displays an extraordinarily diverse population structure both genetically and phenotypically. Yet, to date ...
ORGANISM(S): Trypanosoma cruzi 
2011-08-05 | E-GEOD-23576 | biostudies-arrayexpress
ProteomicsA ‘proteomic ruler’ for protein copy number and concentration estimation without spike-in standards
Absolute protein quantification using mass spectrometry (MS)-based proteomics delivers protein concentrations or copy numbers per cell. Existing methodologies typically require a combination of isotope-labeled spike-in references, cell counting and protein concentration measurements. Here we present...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2014-09-17 | PXD000661 | Pride
Copy numbers Absolute quantification 
TranscriptomicsFine-scale mapping of copy-number alterations with massively parallel sequencing
In order to benchmark the reproducibility of Affymetrix 238K Sty arrays for detecting copy-number alterations. We performed replicate hybridizations of 3 tumor cell lines and 2 paired normal cell lines obtained from the American Type Culture Collection (ATCC). We calculated copy numbers at each SNP...
ORGANISM(S): Homo sapiens 
2008-11-13 | E-GEOD-12019 | biostudies-arrayexpress
TranscriptomicsHigh-resolution mapping of copy-number alterations with massively parallel sequencing
In order to benchmark the reproducibility of Affymetrix Genome-Wide Human SNP Array 6.0 for detecting copy-number alterations, we performed replicate hybridizations of 3 tumor cell lines and 2 paired normal cell lines obtained from the American Type Culture Collection (ATCC). We calculated copy numb...
ORGANISM(S): Homo sapiens 
2008-11-13 | E-GEOD-13372 | 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
TranscriptomicsCopy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans
Background: Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain. Results: We have used array comparative genomic...
ORGANISM(S): Caenorhabditis elegans 
2010-05-17 | E-GEOD-19440 | biostudies-arrayexpress
TranscriptomicsNormalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Methods developed for normalization of WGG arrays have mostly focused on diploid, norma...
ORGANISM(S): Homo sapiens 
2008-10-04 | E-GEOD-11977 | biostudies-arrayexpress
ProteomicsProteogenomic analysis demonstrates increased blaOXA-48 copy numbers and OmpK36 loss as contributors of carbapenem resistance in Klebsiella pneumoniae
Antimicrobial resistance (AMR) arises from complex genetic and regulatory changes, including single mutations, gene acquisitions or cumulative effects. Advancements in genomics and proteomics facilitate more comprehensive understanding of the mechanisms behind antimicrobial resistance. In this study...
ORGANISM(S): Klebsiella pneumoniae 
2025-06-06 | PXD061983 | Pride
Klebsiella pneumoniae Orbitrap hf Bacteria Lc-msms 
TranscriptomicsComparative genomic hybridization of human cervical cancer tumor samples to calculate absolute DNA copy numbers
Array CGH data were used to achieve absolute DNA copy numbers
ORGANISM(S): Homo sapiens 
2008-12-20 | E-TABM-398 | biostudies-arrayexpress
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