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GenomicsChip-Seq of human jurkat cell line to investigate genome-wide mapping of in vivo protein-DNA interactions
In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ...
ORGANISM(S): Homo sapiens 
2009-08-29 | E-GEOD-13047 | biostudies-arrayexpress
TranscriptomicsSpike-in Experiment for ChIP-chip Simulation
The most widely-used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms and analysis algorithms in a simulated ChIP-chip experiment. M...
ORGANISM(S): Homo sapiens 
2010-05-22 | E-GEOD-9732 | biostudies-arrayexpress
MetabolomicsAn Unbiased Lipid Phenotyping Approach To Study the Genetic Determinants of Lipids and Their Association with Coronary Heart Disease Risk Factors
Direct infusion high-resolution mass spectrometry (DIHRMS) is a novel, high-throughput approach to rapidly and accurately profile hundreds of lipids in human serum without prior chromatography, facilitating in-depth lipid phenotyping for large epidemiological studies to reveal the detailed associati...
2024-02-02 | MTBLS4461 | MetaboLights
TranscriptomicsBiopsies from metastatic Clear Cell Renal Carcinoma before or after treatment with nivolumab
Tumor core needle biopsies from kidney or metastatic sites obtained at trial enrollment i.e. Screen and/or at Cycle 2 Day 8 (i.e.Week 4) from metastatic clear cell RCC patients treated with 0.2mpk, 3mpk or 10mpk (as 2nd or further line of therapy; Arms A,B,C) or 10mpk (as first line therapy; Arm D) ...
ORGANISM(S): Homo sapiens 
2016-05-15 | E-MTAB-3218 | biostudies-arrayexpress
UnknownAn expert consensus for the management of chronic hepatitis B in Asian Americans.
Not available
S-EPMC5900913 | biostudies-literature
GenomicsHigh-throughput sequencing of ES cell lines, ES-derived cells, and fetal and normal livers
Publication title: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions...
ORGANISM(S): Homo sapiens 
2011-05-05 | E-GEOD-29071 | biostudies-arrayexpress
TranscriptomicsSystematic evaluation of variability in simulated ChIP-chip experiments
The most widely-used method for detecting and measuring genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Many tiling array platforms, amplification methods, and analysis algorithms exist for ChIP-chip, but a rigorous assessment...
ORGANISM(S): Homo sapiens 
2008-01-31 | E-GEOD-9842 | biostudies-arrayexpress
TranscriptomicsIllumina gene expression beadchips of human ES cell lines
Publication title: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions...
ORGANISM(S): Homo sapiens 
2011-05-05 | E-GEOD-29070 | biostudies-arrayexpress
TranscriptomicsProtein profiling reveals five principal chromatin types in Drosophila cells
The local protein composition of chromatin is important for the regulation of transcription and other functions. By integrative analysis of genome-wide binding maps of 53 broadly selected chromatin components in Drosophila cells, we show that the genome is segmented into five principal chromatin typ...
ORGANISM(S): Drosophila melanogaster 
2010-10-01 | E-GEOD-22069 | biostudies-arrayexpress
GenomicsHistone modification analysis in TGFbeta/TNFalpha treated A549 spheroid cultures
We studied the extent of chromatin remodeling in an in-vitro model of the epithelial-mesenchymal transition (EMT). EMT is induced in spheroid cultures (3D) using simultaneously two cytokines: TGFbeta and TNFalpha. The epithelial-mesenchymal transition (EMT) is a cellular de-differentiation process t...
ORGANISM(S): Homo sapiens 
2013-09-12 | E-GEOD-42374 | biostudies-arrayexpress
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